diff --git a/Makefile b/Makefile
index 98afc864c400ec0ce47c399f243fc1ffbdde0432..848619b9d4302f3999801ff6b01cd6f1e836aaee 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-TARGET = popins2
+TARGET = popins4snake
BUILD_DIR = ./build
SRC_DIR = ./src
@@ -12,10 +12,6 @@ CC = $(CXX)
# SeqAn
SEQAN_LIB = ./external/seqan-library-2.2.0/include/
-# Include config
--include popins2.config
-TOOLS=-DSAMTOOLS=\"$(SAMTOOLS)\" -DBWA=\"$(BWA)\" -DSICKLE=\"$(SICKLE)\" -DVELVETH=\"$(VELVETH)\" -DVELVETG=\"$(VELVETG)\" -DMINIA=\"$(PWD)/$(MINIA)\"
-
# Date and version number from git
DATE := on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1)
VERSION := 0.0.7-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
@@ -24,7 +20,7 @@ CXXFLAGS += -DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\"
# Compiler flags
CXXFLAGS += -DSEQAN_HAS_ZLIB=1 -DSEQAN_DISABLE_VERSION_CHECK
CXXFLAGS += -W -Wall -pedantic
-CXXFLAGS += -Wno-long-long -Wno-variadic-macros -Wno-unused-result
+CXXFLAGS += -Wno-long-long -Wno-variadic-macros -Wno-unused-result -Wno-class-memaccess -Wno-deprecated-copy -Wno-alloc-size-larger-than
CXXFLAGS += -march=native -DMAX_KMER_SIZE=64
CXXFLAGS += -I$(SEQAN_LIB)
@@ -54,7 +50,7 @@ clean:
rm -f $(OBJS) $(TARGET)
purge:
- rm -f $(OBJS) $(TARGET) *.gfa *.bfg_colors *.fasta *.csv popins2*log
+ rm -f $(OBJS) $(TARGET) *.gfa *.bfg_colors *.fasta *.csv $(TARGET)*log
metaclean:
- rm -f $(TARGET) *.gfa *.bfg_colors *.fasta *.csv popins2*log
+ rm -f $(TARGET) *.gfa *.bfg_colors *.fasta *.csv $(TARGET)*log
diff --git a/external/gatb-minia-pipeline/.gitignore b/external/gatb-minia-pipeline/.gitignore
deleted file mode 100644
index 2f0da3064de246772f37648a451240b933adde8c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-CHANGELOG
-kmergenie
-archive
diff --git a/external/gatb-minia-pipeline/.gitmodules b/external/gatb-minia-pipeline/.gitmodules
deleted file mode 100644
index f67bb4b4d19423a1f372f9de01afc1837127a664..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "BESST"]
- path = BESST
- url = https://github.com/ksahlin/BESST.git
diff --git a/external/gatb-minia-pipeline/BESST/BESST/Contig.py b/external/gatb-minia-pipeline/BESST/BESST/Contig.py
deleted file mode 100644
index 1ced089f9e87ab5dd56e91b73da2d4939cc1c232..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/Contig.py
+++ /dev/null
@@ -1,38 +0,0 @@
-'''
-Created on Sep 29, 2011
-
-@author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
-'''
-
-
-class contig(object):
- __slots__ = ('name', 'scaffold', 'direction', 'position', 'length',
- 'coverage', 'repeat', 'is_haplotype', 'sequence')
-
- def __init__(self, contig_name, contig_scaffold=None , contig_direction=None,
- contig_position=None, contig_length=None, contig_coverage=None,
- contig_repeat=False, contig_haplotype=False, contig_sequence=None):
- self.name = contig_name
- self.scaffold = contig_scaffold
- self.direction = contig_direction
- self.position = contig_position
- self.length = contig_length
- self.sequence = contig_sequence
- self.coverage = contig_coverage
- self.repeat = contig_repeat
- self.is_haplotype = contig_haplotype
diff --git a/external/gatb-minia-pipeline/BESST/BESST/CreateGraph.py b/external/gatb-minia-pipeline/BESST/BESST/CreateGraph.py
deleted file mode 100644
index f86c1b7e4b2ec0ccf8de09f72ef577dae74f49c5..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/CreateGraph.py
+++ /dev/null
@@ -1,847 +0,0 @@
-'''
- Created on Sep 29, 2011
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-import sys
-import os
-from collections import defaultdict
-from math import pi
-from time import time
-
-from scipy.stats import ks_2samp
-import networkx as nx
-
-import Contig
-import Scaffold
-from Parameter import counters
-from mathstats.normaldist import normal
-import GenerateOutput as GO
-from mathstats.normaldist.truncatedskewed import param_est
-import errorhandle
-import plots
-
-
-
-
-def PE(Contigs, Scaffolds, Information, C_dict, param, small_contigs, small_scaffolds, bam_file):
- G = nx.Graph()
- G_prime = nx.Graph() # If we want to do path extension with small contigs
- print >> Information, 'Parsing BAM file...'
-
- ##### Initialize contig and scaffold objects ######
-
- if param.first_lib:
- start_init = time()
- InitializeObjects(bam_file, Contigs, Scaffolds, param, Information, G_prime, small_contigs, small_scaffolds, C_dict)
- print >> Information, 'Time initializing BESST objects: ', time() - start_init
-
- else:
- #Clean contig_library/scaffold_library
- start_clean = time()
- CleanObjects(Contigs, Scaffolds, param, Information, small_contigs, small_scaffolds)
- print >> Information, 'Time cleaning BESST objects for next library: ', time() - start_clean
-
- print >> Information, 'Nr of contigs/scaffolds included in scaffolding: ' + str(len(Scaffolds)) #,Scaffolds.keys()
- if len(Scaffolds) == 0:
- if not os.path.isfile(param.output_directory + '/repeats.fa'):
- repeat_file = open(param.output_directory + '/repeats.fa', 'w')
- return(G, G_prime)
-
- ### initialize graph objects two nodes per contig "left" and "right" node. ###
- tot_start = time()
-
- if param.no_score:
- # Only do path search
- #small contig graph contains all scaffolds
- InitializeGraph(small_scaffolds, G_prime, Information)
- InitializeGraph(Scaffolds, G_prime, Information)
- elif param.extend_paths:
- # do scoring and extend paths
- InitializeGraph(Scaffolds, G, Information)
- #small contig graph contains all scaffolds
- InitializeGraph(small_scaffolds, G_prime, Information)
- InitializeGraph(Scaffolds, G_prime, Information)
- else:
- # only do scoring
- InitializeGraph(Scaffolds, G, Information)
- print >> Information, 'Total time elapsed for initializing Graph: ', time() - tot_start
-
- #for coverage computation
- cont_aligned_len = {}
- for contig in Contigs:
- cont_aligned_len[contig] = [0, Contigs[contig].length]
-
- #if param.extend_paths:
- for contig in small_contigs:
- cont_aligned_len[contig] = [0, small_contigs[contig].length]
-
- #initialize counters for library
- counter = counters(0, 0, 0, 0, -1, -1, 0)
- fishy_edges = defaultdict(int)
- ctr = 0
- # Create the link edges in the graph by fetching info from bam file
- print >> Information, 'Reading bam file and creating scaffold graph...'
- staart = time()
-
- if param.development:
- import guppy
- h = guppy.hpy()
- before_ctg_graph = h.heap()
- print 'Just before creating contig graph:\n{0}\n'.format(before_ctg_graph)
-
- for alignedread in bam_file:
- # try: #check that read is aligned OBS: not with is_unmapped since this flag is fishy for e.g. BWA
- # contig1 = bam_file.getrname(alignedread.rname)
- # contig2 = bam_file.getrname(alignedread.mrnm)
- # except ValueError:
- # continue
-
- try:
- contig1 = param.contig_index[alignedread.rname]
- contig2 = param.contig_index[alignedread.mrnm]
- #assert contig1 == contig1_old
- #assert contig2 == contig2_old
- except KeyError:
- continue
-
- #TODO:Repeats (and haplotypes) may have been singled out, we need this statement (or a smarter version of it)
- if (contig1 in Contigs or contig1 in small_contigs) and (contig2 in Contigs or contig2 in small_contigs):
- pass
- else:
- continue
-
- #TODO: this if-statement is an ad hoc implementation to deal with BWA's buggy SAM-flag reporting
- #if BWA fixes this -> remove this statement. If the links in fishy edges is equal to or ore than
- #the links in the graph G or G'. The edge will be removed.
- if alignedread.is_unmapped and alignedread.is_read1: # and contig1 != contig2:
- #Some BWA error in mappings can still slip through, these edges are caracterized by very few links
- try:
- cont_obj1 = small_contigs[contig1]
- scaf_obj1 = small_scaffolds[cont_obj1.scaffold]
- except KeyError:
- cont_obj1 = Contigs[contig1]
- scaf_obj1 = Scaffolds[cont_obj1.scaffold]
- try:
- cont_obj2 = small_contigs[contig2]
- scaf_obj2 = small_scaffolds[cont_obj2.scaffold]
- except KeyError:
- cont_obj2 = Contigs[contig2]
- scaf_obj2 = Scaffolds[cont_obj2.scaffold]
-
- if scaf_obj2.name != scaf_obj1.name:
- (side1, side2) = CheckDir(cont_obj1, cont_obj2, alignedread,param)
- #get scaffold name for contig
- s1 = Contigs[contig1].scaffold if contig1 in Contigs else small_contigs[contig1].scaffold
- s2 = Contigs[contig2].scaffold if contig2 in Contigs else small_contigs[contig2].scaffold
- fishy_edges[((s1, side1), (s2, side2))] += 1
- fishy_edges[((s2, side2), (s1, side1))] += 1
- ctr += 1
-
- ## add to coverage computation if contig is still in the list of considered contigs
- #print contig1, contig2, alignedread.is_read2
- cont_aligned_len[contig1][0] += alignedread.qlen
- if contig1 != contig2 and alignedread.mapq == 0:
- counter.non_unique += 1 # check how many non unique reads out of the useful ones (mapping to two different contigs)
-
- if contig1 != contig2 and alignedread.is_read2 and not alignedread.is_unmapped and alignedread.mapq >= param.min_mapq:
- if contig1 in Contigs and contig2 in Contigs and Contigs[contig2].scaffold != Contigs[contig1].scaffold:
- cont_obj1 = Contigs[contig1]
- cont_obj2 = Contigs[contig2]
- scaf_obj1 = Scaffolds[cont_obj1.scaffold]
- scaf_obj2 = Scaffolds[cont_obj2.scaffold]
- if not param.no_score:
- is_dupl = CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G, param, alignedread, counter, contig1, contig2)
- else:
- is_dupl = CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2, save_obs=False)
-
- if param.extend_paths and not is_dupl and not param.no_score:
- counter.prev_obs1 = -1
- counter.prev_obs2 = -1
- CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2, save_obs=False)
- elif param.extend_paths:
- try:
- cont_obj1 = small_contigs[contig1]
- scaf_obj1 = small_scaffolds[cont_obj1.scaffold]
- value1 = 1
- except KeyError:
- cont_obj1 = Contigs[contig1]
- scaf_obj1 = Scaffolds[cont_obj1.scaffold]
- value1 = 0
- try:
- cont_obj2 = small_contigs[contig2]
- scaf_obj2 = small_scaffolds[cont_obj2.scaffold]
- value2 = 1
- except KeyError:
- cont_obj2 = Contigs[contig2]
- scaf_obj2 = Scaffolds[cont_obj2.scaffold]
- value2 = 0
- if value1 and value2 and scaf_obj1 != scaf_obj2:
- CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2, save_obs=False)
- elif value1 and not value2:
- CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2,save_obs=False)
- elif not value1 and value2:
- CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2,save_obs=False)
-
-
- elif contig1 in Contigs and contig2 in Contigs and Contigs[contig2].scaffold != Contigs[contig1].scaffold:
-########################Use to validate scaffold in previous step here ############
- pass
- print >> Information, 'ELAPSED reading file:', time() - staart
- print >> Information, 'NR OF FISHY READ LINKS: ', ctr
-
- print >> Information, 'Number of USEFUL READS (reads mapping to different contigs uniquly): ', counter.count
- print >> Information, 'Number of non unique reads (at least one read non-unique in read pair) that maps to different contigs (filtered out from scaffolding): ', counter.non_unique
- print >> Information, 'Reads with too large insert size from "USEFUL READS" (filtered out): ', counter.reads_with_too_long_insert
- print >> Information, 'Initial number of edges in G (the graph with large contigs): ', len(G.edges())
- print >> Information, 'Initial number of edges in G_prime (the full graph of all contigs before removal of repats): ', len(G_prime.edges())
-
- if param.detect_duplicate:
- print >> Information, 'Number of duplicated reads indicated and removed: ', counter.nr_of_duplicates
-
- if param.development:
- h = guppy.hpy()
- after_ctg_graph = h.heap()
- print 'Just after creating contig graph:\n{0}\n'.format(after_ctg_graph)
-
-
-##### Calc coverage for all contigs with current lib here #####
- sum_x = 0
- sum_x_sq = 0
- n = 0
- cov = []
- leng = []
- for contig in cont_aligned_len:
- cont_coverage = cont_aligned_len[contig][0] / float(cont_aligned_len[contig][1])
- try:
- Contigs[contig].coverage = cont_coverage
- cov.append(cont_coverage)
- leng.append(Contigs[contig].length)
- except KeyError:
- small_contigs[contig].coverage = cont_coverage
- cov.append(cont_coverage)
- leng.append(small_contigs[contig].length)
-
-
- sum_x += cont_coverage
- sum_x_sq += cont_coverage ** 2
- n += 1
-
- del cont_aligned_len
-
- mean_cov, std_dev_cov = CalculateMeanCoverage(Contigs, Information, param)
- param.mean_coverage = mean_cov
- param.std_dev_coverage = std_dev_cov
- if param.first_lib:
- Contigs, Scaffolds, G = RepeatDetector(Contigs, Scaffolds, G, param, G_prime, small_contigs, small_scaffolds, Information)
-
- print >> Information, 'Number of edges in G (after repeat removel): ', len(G.edges())
- print >> Information, 'Number of edges in G_prime (after repeat removel): ', len(G_prime.edges())
-
- ### Remove edges created by false reporting of BWA ###
- RemoveBugEdges(G, G_prime, fishy_edges, param, Information)
-
- print >> Information, 'Number of edges in G (after filtering for buggy flag stats reporting): ', len(G.edges())
- print >> Information, 'Number of edges in G_prime (after filtering for buggy flag stats reporting): ', len(G_prime.edges())
-
- if param.development:
- h = guppy.hpy()
- after_coverage = h.heap()
- print 'Just after calc coverage:\n{0}\n'.format(after_coverage)
-
- ## Score edges in graph
- plot = 'G'
- if not param.no_score:
- GiveScoreOnEdges(G, Scaffolds, small_scaffolds, Contigs, param, Information, plot)
- #plot = 'G_prime'
- #GiveScoreOnEdges(G_prime, Scaffolds, small_scaffolds, Contigs, param, Information, plot)
-
-
- #Remove all edges with link support less than 3 to be able to compute statistics:
- cntr_sp = 0
- for edge in G_prime.edges():
- if G_prime[edge[0]][edge[1]]['nr_links'] != None:
- if G_prime[edge[0]][edge[1]]['nr_links'] < param.edgesupport:
- G_prime.remove_edge(edge[0], edge[1])
- cntr_sp += 1
- print >> Information, 'Number of fishy edges in G_prime', cntr_sp
-
- print >> Information, 'Number of edges in G_prime (after removing edges under -e threshold (if not specified, default is -e 3): ', len(G_prime.edges())
-
- if param.development:
- h = guppy.hpy()
- after_scoring = h.heap()
- print 'After scoring:\n{0}\n'.format(after_scoring)
-
- return(G, G_prime)
-
-
-def GiveScoreOnEdges(G, Scaffolds, small_scaffolds, Contigs, param, Information, plot):
-
- span_score_obs = []
- std_dev_score_obs = []
- gap_obs = []
- nr_link_obs = []
- cnt_sign = 0
-
- if param.print_scores:
- score_file = open(os.path.join(param.output_directory,"score_file_pass_{0}.tsv".format(param.pass_number)), "w")
- print >>score_file, "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}".format("scf1/ctg1", "o1", "scf2/ctg2", "o2", "gap", "link_variation_score", "link_dispersity_score", "number_of_links")
-
- for edge in G.edges():
- mean_ = 0
- std_dev = 0
- if G[edge[0]][edge[1]]['nr_links'] != None:
- n = G[edge[0]][edge[1]]['nr_links']
- obs_squ = G[edge[0]][edge[1]]['obs_sq']
- mean_ = G[edge[0]][edge[1]]['obs'] / float(n)
- data_observation = (n * param.mean_ins_size - G[edge[0]][edge[1]]['obs']) / float(n)
- try:
- len1 = Scaffolds[ edge[0][0] ].s_length
- except KeyError:
- len1 = small_scaffolds[ edge[0][0] ].s_length
- try:
- len2 = Scaffolds[ edge[1][0] ].s_length
- except KeyError:
- len2 = small_scaffolds[ edge[1][0] ].s_length
- if 2 * param.std_dev_ins_size < len1 and 2 * param.std_dev_ins_size < len2:
- gap = param_est.GapEstimator(param.mean_ins_size, param.std_dev_ins_size, param.read_len, mean_, len1, len2)
- else:
- gap = data_observation
-
- G[edge[0]][edge[1]]['gap'] = int(gap)
- if -gap > len1 or -gap > len2:
- G[edge[0]][edge[1]]['score'] = 0
- continue
-
- #std_dev_d_eq_0 = param_est.tr_sk_std_dev(param.mean_ins_size, param.std_dev_ins_size, param.read_len, len1, len2, gap)
-
- if 2 * param.std_dev_ins_size < len1 and 2 * param.std_dev_ins_size < len2:
- std_dev_d_eq_0 = param_est.tr_sk_std_dev(param.mean_ins_size, param.std_dev_ins_size, param.read_len, len1, len2, gap)
- else:
- std_dev_d_eq_0 = 2 ** 32
-
- try:
- std_dev = ((obs_squ - n * mean_ ** 2) / (n - 1)) ** 0.5
- #chi_sq = (n - 1) * (std_dev ** 2 / std_dev_d_eq_0 ** 2)
- except ZeroDivisionError:
- std_dev = 2 ** 32
- #chi_sq = 0
-
-
- try:
- l1 = G[edge[0]][edge[1]][Scaffolds[edge[0][0]].name]
- del G[edge[0]][edge[1]][Scaffolds[edge[0][0]].name]
- except KeyError:
- l1 = G[edge[0]][edge[1]][small_scaffolds[edge[0][0]].name]
- del G[edge[0]][edge[1]][small_scaffolds[edge[0][0]].name]
- try:
- l2 = G[edge[0]][edge[1]][Scaffolds[edge[1][0]].name]
- del G[edge[0]][edge[1]][Scaffolds[edge[1][0]].name]
- except KeyError:
- l2 = G[edge[0]][edge[1]][small_scaffolds[edge[1][0]].name]
- del G[edge[0]][edge[1]][small_scaffolds[edge[1][0]].name]
-
-
- l1.sort()
- n_obs = len(l1)
- l1_mean = sum(l1) / float(n_obs)
- #l1_median = l1[len(l1) / 2]
- l1 = map(lambda x: x - l1_mean, l1)
- #l1 = map(lambda x: x - l1_median, l1)
- max_obs2 = max(l2)
- l2.sort(reverse=True)
- l2 = map(lambda x: abs(x - max_obs2), l2)
- l2_mean = sum(l2) / float(n_obs)
- #l2_median = l2[len(l2) / 2]
- l2 = map(lambda x: x - l2_mean, l2)
- #l2 = map(lambda x: x - l2_median, l2)
- KS_statistic, p_value = ks_2samp(l1, l2)
-
-
- #M_W_statistic, p_val = mannwhitneyu(l1, l2)
-
- #diff = map(lambda x: abs(abs(x[1]) - abs(x[0])), zip(l1, l2))
- #sc = sum(diff) / len(diff)
-
- if len(l1) < 3:
- span_score = 0
- else:
- span_score = 1 - KS_statistic
-
- try:
- std_dev_score = min(std_dev / std_dev_d_eq_0, std_dev_d_eq_0 / std_dev) #+ span_score #+ min(n/E_links, E_links/float(n))
- except ZeroDivisionError:
- std_dev_score = 0
- sys.stderr.write(str(std_dev) + ' ' + str(std_dev_d_eq_0) + ' ' + str(span_score) + '\n')
-
- G[edge[0]][edge[1]]['score'] = std_dev_score + span_score if std_dev_score > 0.5 and span_score > 0.5 else 0
-
- if param.plots:
- span_score_obs.append(span_score)
- std_dev_score_obs.append(std_dev_score)
- gap_obs.append(gap)
- nr_link_obs.append(n_obs)
-
- if param.print_scores:
- if edge[0][1] == 'R':
- contig_objects = Scaffolds[edge[0][0]].contigs
- contig_names = map(lambda x: x.name, contig_objects)
- scf1 = ";".join(contig_names)
- contig_directions_bool = map(lambda x: x.direction, contig_objects)
- contig_directions1 = ";".join(map(lambda x: '+' if True else '-', contig_directions_bool))
-
- else:
- contig_objects = Scaffolds[edge[0][0]].contigs[::-1]
- contig_names = map(lambda x: x.name, contig_objects)
- scf1 =";".join(contig_names)
- contig_directions_bool = map(lambda x: x.direction, contig_objects)
- contig_directions1 = ";".join(map(lambda x: '+' if False else '-', contig_directions_bool))
-
- if edge[1][1] == 'L':
- contig_objects = Scaffolds[edge[1][0]].contigs
- contig_names = map(lambda x: x.name, contig_objects)
- scf2 =";".join(contig_names)
- contig_directions_bool = map(lambda x: x.direction, contig_objects)
- contig_directions2 = ";".join(map(lambda x: '+' if True else '-', contig_directions_bool))
-
- else:
- contig_objects = Scaffolds[edge[1][0]].contigs[::-1]
- contig_names = map(lambda x: x.name, contig_objects)
- scf2 =";".join(contig_names)
- contig_directions_bool = map(lambda x: x.direction, contig_objects)
- contig_directions2 = ";".join(map(lambda x: '+' if False else '-', contig_directions_bool))
-
- print >>score_file, "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}".format(scf1, contig_directions1, scf2, contig_directions2, gap, std_dev_score, span_score, n_obs)
-
- if param.print_scores:
- score_file.close()
-
- if param.plots:
- plots.histogram(span_score_obs, param, bins=20, x_label='score', y_label='frequency', title='Dispersity_score_distribuion' + plot + '.' + param.bamfile.split('/')[-1])
- plots.histogram(std_dev_score_obs, param, bins=20, x_label='score', y_label='frequency', title='Standard_deviation_score_distribuion' + plot + '.' + param.bamfile.split('/')[-1])
- plots.dot_plot(std_dev_score_obs, span_score_obs, param, x_label='std_dev_score_obs', y_label='span_score_obs', title='Score_correlation' + plot + '.' + param.bamfile.split('/')[-1])
- plots.dot_plot(std_dev_score_obs, gap_obs, param, x_label='std_dev_score_obs', y_label='estimated gap size', title='Gap_to_sigma' + plot + '.' + param.bamfile.split('/')[-1])
- plots.dot_plot(span_score_obs, gap_obs, param, x_label='span_score_obs', y_label='estimated gap size', title='Gap_to_span' + plot + '.' + param.bamfile.split('/')[-1])
- plots.dot_plot(span_score_obs, nr_link_obs, param, x_label='span_score_obs', y_label='Number links', title='Obs_to_span' + plot + '.' + param.bamfile.split('/')[-1])
-
- for edge in G.edges():
- if G[edge[0]][edge[1]]['nr_links'] != None:
- try:
- G[edge[0]][edge[1]]['score']
- except KeyError:
- sys.stderr.write(str(G[edge[0]][edge[1]]) + ' ' + str(Scaffolds[edge[0][0]].s_length) + ' ' + str(Scaffolds[edge[1][0]].s_length))
- print >> Information, 'Number of significantly spurious edges:', cnt_sign
-
- return()
-
-
-
-
-
-def CheckDir(cont_obj1, cont_obj2, alignedread, param):
- (read_dir, mate_dir) = (not alignedread.is_reverse, not alignedread.mate_is_reverse)
- cont_dir1 = cont_obj1.direction #if pos : L if neg: R
- #position2 cont2/scaf2
- cont_dir2 = cont_obj2.direction
- if param.orientation == 'fr':
- (obs1, obs2, scaf_side1, scaf_side2) = PosDirCalculatorPE(cont_dir1, read_dir, 0, 0, 0, 0, cont_dir2, mate_dir, 0, 0, 0, 0, 0)
- else:
- (obs1, obs2, scaf_side1, scaf_side2) = PosDirCalculatorMP(cont_dir1, read_dir, 0, 0, 0, 0, cont_dir2, mate_dir, 0, 0, 0, 0, 0)
-
- return(scaf_side1, scaf_side2)
-
-def RemoveBugEdges(G, G_prime, fishy_edges, param, Information):
- edges_removed = 0
- for edge_tuple, nr_links in fishy_edges.items():
- if param.extend_paths:
- if edge_tuple[1] in G_prime and edge_tuple[0] in G_prime[edge_tuple[1]]:
- if nr_links >= G_prime[edge_tuple[0]][edge_tuple[1]]['nr_links']:
- G_prime.remove_edge(edge_tuple[0], edge_tuple[1])
- edges_removed += 1
- if edge_tuple[1] in G and edge_tuple[0] in G[edge_tuple[1]]:
- if nr_links >= G[edge_tuple[0]][edge_tuple[1]]['nr_links']:
- G.remove_edge(edge_tuple[0], edge_tuple[1])
- else:
- if edge_tuple[1] in G and edge_tuple[0] in G[edge_tuple[1]]:
- if nr_links >= G[edge_tuple[0]][edge_tuple[1]]['nr_links']:
- G.remove_edge(edge_tuple[0], edge_tuple[1])
- edges_removed += 1
- print >> Information, 'Number of BWA buggy edges removed: ', edges_removed
- del fishy_edges
- return()
-
-def InitializeGraph(dict_with_scaffolds, graph, Information):
- cnt = 1
- start1 = time()
- for scaffold_ in dict_with_scaffolds:
- graph.add_edge((scaffold_, 'L'), (scaffold_, 'R'), nr_links=None) #this is a scaffold object but can be both a single contig or a scaffold.
- graph.node[(scaffold_, 'L')]['length'] = dict_with_scaffolds[scaffold_].s_length
- graph.node[(scaffold_, 'R')]['length'] = dict_with_scaffolds[scaffold_].s_length
- if cnt % 100000 == 0 and cnt > 0:
- elapsed = time() - start1
- print >> Information, 'Total nr of keys added: ', cnt, 'Time for adding last 100 000 keys: ', elapsed
- start1 = time()
- cnt += 1
- return()
-
-# def constant_large():
-# return 2 ** 32
-# def constant_small():
-# return -1
-
-def InitializeObjects(bam_file, Contigs, Scaffolds, param, Information, G_prime, small_contigs, small_scaffolds, C_dict):
- singeled_out = 0
- contig_threshold = param.contig_threshold
- cont_lengths = bam_file.lengths
- cont_lengths = [int(nr) for nr in cont_lengths] #convert long to int object
- cont_names = bam_file.references
-
- #Calculate NG50 and LG 50
- param.tot_assembly_length = sum(cont_lengths)
- sorted_lengths = sorted(cont_lengths, reverse=True)
- N50, L50 = CalculateStats(sorted_lengths, [], param, Information)
- param.current_L50 = L50
- param.current_N50 = N50
- #extend_paths = param.extend_paths
- counter = 0
- start = time()
- for i in range(0, len(cont_names)):
- counter += 1
- if counter % 100000 == 0:
- print >> Information, 'Time adding 100k keys', time() - start
- start = time()
- if cont_names[i] not in C_dict:
- #errorhandle.unknown_contig(cont_names[i])
- continue
-
- if cont_lengths[i] >= contig_threshold:
- C = Contig.contig(cont_names[i]) # Create object contig
- C.length = cont_lengths[i]
- C.sequence = C_dict[cont_names[i]]
- del C_dict[cont_names[i]]
- scaf_length = C.length # Initially, scaffold consists of only this contig
- C.direction = True # always in same direction first, False=reverse
- C.position = 0 #position always 0
- #C.links = {}
- Contigs[C.name] = C # Create a dict with name as key and the object container as value
- S = Scaffold.scaffold(param.scaffold_indexer, [C], scaf_length) # Create object scaffold
- Scaffolds[S.name] = S
- C.scaffold = S.name
- param.scaffold_indexer += 1
- else:
- if cont_lengths[i] > 0: #In case of contigs with size 0 (due to some error in fasta file)
- C = Contig.contig(cont_names[i]) # Create object contig
- C.length = cont_lengths[i]
- C.sequence = C_dict[cont_names[i]]
- del C_dict[cont_names[i]]
- scaf_length = C.length # Initially, scaffold consists of only this contig
- C.direction = True # always in same direction first, False=reverse
- C.position = 0 #position always 0
- small_contigs[C.name] = C # Create a dict with name as key and the object container as value
- S = Scaffold.scaffold(param.scaffold_indexer, [C], scaf_length) # Create object scaffold
- small_scaffolds[S.name] = S
- C.scaffold = S.name
- param.scaffold_indexer += 1
- singeled_out += 1
- del C_dict
-
-
- print >> Information, 'Nr of contigs that was singeled out due to length constraints ' + str(singeled_out)
- return()
-
-def CleanObjects(Contigs, Scaffolds, param, Information, small_contigs, small_scaffolds):
- singeled_out = 0
- scaf_lengths = [Scaffolds[scaffold_].s_length for scaffold_ in Scaffolds.keys()]
- sorted_lengths = sorted(scaf_lengths, reverse=True)
- scaf_lengths_small = [small_scaffolds[scaffold_].s_length for scaffold_ in small_scaffolds.keys()]
- sorted_lengths_small = sorted(scaf_lengths_small, reverse=True)
- N50, L50 = CalculateStats(sorted_lengths, sorted_lengths_small, param, Information)
- param.current_L50 = L50
- param.current_N50 = N50
- for scaffold_ in Scaffolds.keys(): #iterate over keys in hash, so that we can remove keys while iterating over it
- if Scaffolds[scaffold_].s_length < param.contig_threshold:
- ### Switch from Scaffolds to small_scaffolds (they can still be used in the path extension)
- ### Remove Scaf_obj from Scaffolds and Contig_obj from contigs
- S_obj = Scaffolds[scaffold_]
- list_of_contigs = S_obj.contigs #list of contig objects contained in scaffold object
- GO.ChangeToSmallContigs(Contigs, list_of_contigs, small_contigs)
- scaf_obj = Scaffolds[scaffold_]
- small_scaffolds[scaffold_] = scaf_obj
- del Scaffolds[scaffold_]
- singeled_out += 1
-
- print >> Information, 'Nr of contigs/scaffolds that was singeled out due to length constraints ' + str(singeled_out)
- return()
-
-def CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G, param, alignedread, counter, contig1, contig2, save_obs=True):
- if alignedread.mapq == 0:
- counter.non_unique_for_scaf += 1
- counter.count += 1
- (read_dir, mate_dir) = (not alignedread.is_reverse, not alignedread.mate_is_reverse)
- #Calculate actual position on scaffold here
- #position1 cont/scaf1
- cont_dir1 = cont_obj1.direction #if pos : L if neg: R
- cont1_pos = cont_obj1.position
- readpos = alignedread.pos
- cont1_len = cont_obj1.length
- s1len = scaf_obj1.s_length
- #position2 cont2/scaf2
- cont_dir2 = cont_obj2.direction
- cont2_pos = cont_obj2.position
- matepos = alignedread.mpos
- cont2_len = cont_obj2.length
- s2len = scaf_obj2.s_length
- if param.orientation == 'fr':
- (obs1, obs2, scaf_side1, scaf_side2) = PosDirCalculatorPE(cont_dir1, read_dir, cont1_pos, readpos, s1len, cont1_len, cont_dir2, mate_dir, cont2_pos, matepos, s2len, cont2_len, param.read_len)
- else:
- (obs1, obs2, scaf_side1, scaf_side2) = PosDirCalculatorMP(cont_dir1, read_dir, cont1_pos, readpos, s1len, cont1_len, cont_dir2, mate_dir, cont2_pos, matepos, s2len, cont2_len, param.read_len)
-
- if obs1 == counter.prev_obs1 and obs2 == counter.prev_obs2:
- counter.nr_of_duplicates += 1
- if param.detect_duplicate:
- return(1)
-
- if obs1 + obs2 < param.mean_ins_size + 6 * param.std_dev_ins_size and obs1 > 25 and obs2 > 25:
- if (scaf_obj2.name, scaf_side2) not in G[(scaf_obj1.name, scaf_side1)]:
- G.add_edge((scaf_obj2.name, scaf_side2), (scaf_obj1.name, scaf_side1), nr_links=1, obs=obs1 + obs2)
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs_sq'] = (obs1 + obs2) ** 2
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['observations'] = [obs1+obs2]
-
- if save_obs:
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)][scaf_obj1.name] = [obs1]
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)][scaf_obj2.name] = [obs2]
- elif save_obs:
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['nr_links'] += 1
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs'] += obs1 + obs2
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)][scaf_obj1.name].append(obs1)
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)][scaf_obj2.name].append(obs2)
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs_sq'] += (obs1 + obs2) ** 2
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['observations'].append(obs1+obs2)
-
- else:
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['nr_links'] += 1
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs'] += obs1 + obs2
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs_sq'] += (obs1 + obs2) ** 2
- G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['observations'].append(obs1+obs2)
-
-
- else:
- counter.reads_with_too_long_insert += 1
-
- ## add to haplotype graph here!!
-
- counter.prev_obs1 = obs1
- counter.prev_obs2 = obs2
- return(0)
-
-
-def CalculateStats(sorted_contig_lengths, sorted_contig_lengths_small, param, Information):
- cur_length = 0
- nr_conts = 0
- L50 = 0
- N50 = 0
- for contig_length in sorted_contig_lengths:
- cur_length += contig_length
- nr_conts += 1
- if cur_length >= param.tot_assembly_length / 2.0:
- N50 = contig_length
- L50 = nr_conts
- break
- if N50 == 0:
- for contig_length in sorted_contig_lengths_small:
- cur_length += contig_length
- nr_conts += 1
- if cur_length >= param.tot_assembly_length / 2.0:
- N50 = contig_length
- L50 = nr_conts
- break
- print >> Information, 'L50: ', L50, 'N50: ', N50, 'Initial contig assembly length: ', param.tot_assembly_length
- return(N50, L50)
-
-def CalculateMeanCoverage(Contigs, Information, param):
- # tuples like (cont lenght, contig name)
- list_of_cont_tuples = [(Contigs[contig].length, contig) for contig in Contigs]
- #sorted as longest first
- list_of_cont_tuples = sorted(list_of_cont_tuples, key=lambda tuple: tuple[0], reverse=True)
- #coverages of longest contigs
- longest_contigs = list_of_cont_tuples[:50000]
- cov_of_longest_contigs = [Contigs[contig[1]].coverage for contig in longest_contigs]
- #Calculate mean coverage from the 1000 longest contigs
- n = float(len(cov_of_longest_contigs))
- mean_cov = sum(cov_of_longest_contigs) / n
- # If there is only one contig above the size threshold, n can be 1
- if n==1:
- n+=1
-
- std_dev = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_cov + mean_cov ** 2), cov_of_longest_contigs))) / (n - 1)) ** 0.5
- extreme_obs_occur = True
- print >> Information, 'Mean coverage before filtering out extreme observations = ', mean_cov
- print >> Information, 'Std dev of coverage before filtering out extreme observations= ', std_dev
-
- ## SMOOTH OUT THE MEAN HERE by removing extreme observations ##
- while extreme_obs_occur:
- extreme_obs_occur, filtered_list = RemoveOutliers(mean_cov, std_dev, cov_of_longest_contigs)
- n = float(len(filtered_list))
- try:
- mean_cov = sum(filtered_list) / n
- except ZeroDivisionError:
- break
- std_dev = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_cov + mean_cov ** 2), filtered_list))) / (n - 1)) ** 0.5
- cov_of_longest_contigs = filtered_list
-
- print >> Information, 'Mean coverage after filtering = ', mean_cov
- print >> Information, 'Std coverage after filtering = ', std_dev
- print >> Information, 'Length of longest contig in calc of coverage: ', longest_contigs[0][0]
- print >> Information, 'Length of shortest contig in calc of coverage: ', longest_contigs[-1][0]
-
-
- if param.plots:
- plots.histogram(cov_of_longest_contigs, param, bins=50, x_label='coverage' , y_label='frequency' , title='BESST_cov_1000_longest_cont' + param.bamfile.split('/')[-1])
-
- return(mean_cov, std_dev)
-
-def RemoveOutliers(mean_cov, std_dev, cov_list):
- k = normal.MaxObsDistr(len(cov_list), 0.95)
- filtered_list = list(filter((lambda x : (x < mean_cov + k * std_dev and x < 2 * mean_cov)), cov_list))
- if len(cov_list) > len(filtered_list):
- return(True, filtered_list)
- else:
- return(False, filtered_list)
-
-def RepeatDetector(Contigs, Scaffolds, G, param, G_prime, small_contigs, small_scaffolds, Information):
- param.output_directory
- mean_cov = param.mean_coverage
- std_dev = param.std_dev_coverage
- cov_cutoff = param.cov_cutoff
- Repeats = []
- count_repeats = 0
- count_hapl = 0
- nr_of_contigs = len(Contigs)
- k = normal.MaxObsDistr(nr_of_contigs, 0.95)
- repeat_thresh = max(mean_cov + k * std_dev, 2 * mean_cov - 3*std_dev)
- if cov_cutoff:
- repeat_thresh = cov_cutoff
- print >> Information, 'Detecting repeats..'
- plot_cov_list = []
- for contig in Contigs:
- plot_cov_list.append(Contigs[contig].coverage)
- if Contigs[contig].coverage > repeat_thresh:
- count_repeats += 1
- cont_obj_ref = Contigs[contig]
- Repeats.append(cont_obj_ref)
- scaf_ = Contigs[contig].scaffold
- del Scaffolds[scaf_]
- G.remove_nodes_from([(scaf_, 'L'), (scaf_, 'R')])
- if param.extend_paths:
- G_prime.remove_nodes_from([(scaf_, 'L'), (scaf_, 'R')])
- #TEST DETECTOR
- if param.detect_haplotype and Contigs[contig].coverage < mean_cov / 2.0 + param.hapl_threshold * std_dev: # < mean_cov - 2.5*std_dev:
- count_hapl += 1
- #have indicator of possible haplotype
- Contigs[contig].is_haplotype = True
-
-
-# if param.extend_paths:
- for contig in small_contigs:
- plot_cov_list.append(small_contigs[contig].coverage)
- if small_contigs[contig].coverage > repeat_thresh:
- count_repeats += 1
- cont_obj_ref = small_contigs[contig]
- Repeats.append(cont_obj_ref)
- scaf_ = small_contigs[contig].scaffold
- del small_scaffolds[scaf_]
- G_prime.remove_nodes_from([(scaf_, 'L'), (scaf_, 'R')])
- #TEST DETECTOR
- if param.detect_haplotype and small_contigs[contig].coverage < mean_cov / 2.0 + param.hapl_threshold * std_dev: # < mean_cov - 2.5*std_dev:
- count_hapl += 1
- #have indicator of possible haplotype
- small_contigs[contig].is_haplotype = True
-
-
- if param.plots:
- plotting_ = filter(lambda x: x < 55 , plot_cov_list)
- plots.histogram(plotting_, param, bins=100, x_label='coverage' , y_label='frequency' , title='contigs_coverage' + param.bamfile.split('/')[-1])
-
- GO.PrintOutRepeats(Repeats, Contigs, param.output_directory, small_contigs)
- print >> Information, 'Removed a total of: ', count_repeats, ' repeats. With coverage larger than ', repeat_thresh
- #sys.exit()
- if param.detect_haplotype:
- print >> Information, 'Marked a total of: ', count_hapl, ' potential haplotypes.'
- return(Contigs, Scaffolds, G)
-
-
-
-
-
-def PosDirCalculatorPE(cont_dir1, read_dir, cont1pos, readpos, s1len, cont1_len, cont_dir2, mate_dir, cont2pos, matepos, s2len, cont2_len, read_len):
- if cont_dir1 and read_dir:
- obs1 = s1len - cont1pos - readpos
- scaf_side1 = 'R'
- if cont_dir2 and mate_dir:
- obs2 = s2len - cont2pos - matepos
- scaf_side2 = 'R'
- if (not cont_dir1) and read_dir:
- obs1 = cont1pos + (cont1_len - readpos)
- scaf_side1 = 'L'
- if (not cont_dir2) and mate_dir:
- obs2 = cont2pos + (cont2_len - matepos)
- scaf_side2 = 'L'
- if cont_dir1 and not read_dir:
- obs1 = cont1pos + readpos + read_len
- scaf_side1 = 'L'
- if cont_dir2 and not mate_dir:
- obs2 = cont2pos + matepos + read_len
- scaf_side2 = 'L'
- if not cont_dir1 and not read_dir:
- obs1 = s1len - cont1pos - (cont1_len - readpos - read_len)
- scaf_side1 = 'R'
- if not cont_dir2 and not mate_dir:
- obs2 = s2len - cont2pos - (cont2_len - matepos - read_len)
- scaf_side2 = 'R'
- return(int(obs1), int(obs2), scaf_side1, scaf_side2)
-
-def PosDirCalculatorMP(cont_dir1, read_dir, cont1pos, readpos, s1len, cont1_len, cont_dir2, mate_dir, cont2pos, matepos, s2len, cont2_len, read_len):
- if cont_dir1 and not read_dir:
- obs1 = s1len - cont1pos - readpos
- scaf_side1 = 'R'
- if cont_dir2 and not mate_dir:
- obs2 = s2len - cont2pos - matepos
- scaf_side2 = 'R'
- if (not cont_dir1) and not read_dir:
- obs1 = cont1pos + (cont1_len - readpos)
- scaf_side1 = 'L'
- if (not cont_dir2) and not mate_dir:
- obs2 = cont2pos + (cont2_len - matepos)
- scaf_side2 = 'L'
- if cont_dir1 and read_dir:
- obs1 = cont1pos + readpos + read_len
- scaf_side1 = 'L'
- if cont_dir2 and mate_dir:
- obs2 = cont2pos + matepos + read_len
- scaf_side2 = 'L'
- if not cont_dir1 and read_dir:
- obs1 = s1len - cont1pos - (cont1_len - readpos - read_len)
- scaf_side1 = 'R'
- if not cont_dir2 and mate_dir:
- obs2 = s2len - cont2pos - (cont2_len - matepos - read_len)
- scaf_side2 = 'R'
- return(int(obs1), int(obs2), scaf_side1, scaf_side2)
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/ExtendLargeScaffolds.py b/external/gatb-minia-pipeline/BESST/BESST/ExtendLargeScaffolds.py
deleted file mode 100644
index 4981fa298fa0792c5eb4af2cf397d4265f0e1078..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/ExtendLargeScaffolds.py
+++ /dev/null
@@ -1,441 +0,0 @@
-
-'''
- Created on Jun 21, 2012
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-import time
-import networkx as nx
-from collections import defaultdict
-import multiprocessing as mp
-import heapq
-
-def ScorePaths(G, paths, all_paths, param):
- if len(paths) == 0:
- return ()
-
- def calculate_connectivity(path, G):
- """
- Contig ends has even or odd numbered placements (index) in the path list. In case
- of contamination, good links are between an even to an odd indexed contig-end, or vice versa.
-
- """
- bad_link_weight = 0
- good_link_weight = 0
- links_not_in_path = 0
- links_wrong_orientation_in_path = 0
- even, odd = path[::2], path[1::2]
- nodes_even = set(even)
- nodes_odd = set(odd)
- visited = set()
- for i, node in enumerate(path):
- for nbr in G.neighbors(node):
- if i % 2 == 0 and node[0] != nbr[0]:
- if nbr in nodes_odd:
- if nbr not in visited:
- good_link_weight += G[node][nbr]['nr_links']
- else:
- pass
- else:
- bad_link_weight += G[node][nbr]['nr_links']
- elif i % 2 == 1 and node[0] != nbr[0]:
- if nbr not in nodes_even:
- bad_link_weight += G[node][nbr]['nr_links']
- elif nbr not in visited:
- bad_link_weight += G[node][nbr]['nr_links']
- visited.add(node)
- good_link_weight = good_link_weight
- bad_link_weight = bad_link_weight
- try:
- score = good_link_weight / float(bad_link_weight)
- except ZeroDivisionError:
- score = good_link_weight
-
- return score, bad_link_weight
-
-
- def calculate_connectivity_contamination(path, G):
- """
- Contig ends has even or odd numbered placements (index) in the path list. In case
- of contamination, good links are between an even to an odd indexed contig-end, or vice versa.
-
- """
- bad_link_weight = 0
- good_link_weight = 0
- links_not_in_path = 0
- links_wrong_orientation_in_path = 0
- even, odd = path[::2], path[1::2]
- nodes_even = set(even)
- nodes_odd = set(odd)
- for i, node in enumerate(path):
- for nbr in G.neighbors(node):
- if i % 2 == 0 and node[0] != nbr[0]:
- if nbr in nodes_odd:
- good_link_weight += G[node][nbr]['nr_links']
- else:
- bad_link_weight += G[node][nbr]['nr_links']
- elif i % 2 == 1 and node[0] != nbr[0]:
- if nbr in nodes_even:
- good_link_weight += G[node][nbr]['nr_links']
- else:
- bad_link_weight += G[node][nbr]['nr_links']
- good_link_weight = good_link_weight/2
- bad_link_weight = bad_link_weight
-
- # ###############
-
-
- try:
- score = good_link_weight / float(bad_link_weight)
- except ZeroDivisionError:
- score = good_link_weight
-
- return score, bad_link_weight
-
-
- #print '\nSTARTING scoring paths:'
- for path in paths:
- #path = path_[0]
- #path_len = path_[1]
- #calculate spanning score s_ci
- if param.contamination_ratio:
- score, bad_link_weight = calculate_connectivity_contamination(path, G)
- else:
- score, bad_link_weight = calculate_connectivity(path, G)
-
-
- if param.no_score and score >= param.score_cutoff:
- all_paths.append([score, bad_link_weight, path, len(path)])
- #Insert_path(all_paths, score, path , bad_link_weight, path_len)
- elif len(path) > 2 and score >= param.score_cutoff: #startnode and end node are not directly connected
- all_paths.append([score, bad_link_weight, path, len(path)])
- #Insert_path(all_paths, score, path , bad_link_weight, path_len)
-
- return ()
-
-def find_all_paths_for_start_node_BFS(graph, start, end, already_visited, is_withing_scaf, max_path_length_allowed, param):
- path = []
- paths = []
- if start[1] == 'L':
- forbidden = set()
- forbidden.add((start[0], 'R'))
- else:
- forbidden = set()
- forbidden.add((start[0], 'L'))
-
- #Joining within scaffolds
- if is_withing_scaf:
- element = end.pop()
- end.add(element)
- if element[1] == 'L':
- forbidden.add((element[0], 'R'))
- else:
- forbidden.add((element[0], 'L'))
-
-
- #TODO: Have length criteria that limits the path lenght due to complecity reasons. Can also identify strange
- #links by looking how many neighbors a contig has and how mych the library actually can span
- path_len = 0
- queue = [(start, path, path_len)]#, sum_path)]
- #prev_node = start
- counter = 0
- while queue:
- #prev_node = start
- counter += 1
- #if counter % 100 == 0:
- # print 'Potential paths:', counter, 'paths found: ', len(paths)
- if counter > param.path_threshold or len(path) > 100:
- print 'Hit path_threshold of {0} iterations! consider increase --iter <int> parameter to over {0} if speed of BESST is not a problem. Standard increase is, e.g., 2-10x of current value'.format(param.path_threshold)
- break
-
- start, path, path_len = queue.pop() #start, end, path, sum_path = queue.pop()
- try:
- prev_node = path[-1]
- except IndexError:
- prev_node = start
- path = path + [start]
- path_len = len(path)
- #print 'PATH', path ,'end', end
- if path_len > max_path_length_allowed: #All possible paths can be exponential!! need something to stop algorithm in time
- continue
- #if score < score_best_path: # need something to stop a bad path
- # continue
- if start in already_visited or start in forbidden:
- continue
-
- if start in end:
- # if (start_node, start) in nodes_present_in_path:
- # nodes_present_in_path[(start_node, start)] = nodes_present_in_path[(start_node, start)].union(path)
- # else:
- # nodes_present_in_path[(start_node, start)] = set(path)
- paths.append((path, path_len))
- continue
-
-
- if prev_node[0] != start[0]:
- if start[1] == 'L' and (start[0], 'R') not in forbidden:
- queue.append(((start[0], 'R'), path, path_len)) #, sum_path + graph[start][(start[0], 'R')]['nr_links']))
- elif start[1] == 'R' and (start[0], 'L') not in forbidden:
- queue.append(((start[0], 'L'), path, path_len))#, sum_path + graph[start][(start[0], 'L')]['nr_links']))
- else:
- for node in set(graph[start]).difference(path):
- if node not in forbidden: # and node not in already_visited:
- try: # if last node (i.e. "end") it is not present in small_scaffolds and it should not be included in the length
- queue.append((node, path, path_len + graph[node[0]]['length'])) # small_scaffolds[node[0]].s_length)) #
- except KeyError:
- queue.append((node, path, path_len))
-
- return paths
-
-def find_all_paths_for_start_node_BFS_improved(graph, start, end, already_visited, is_withing_scaf, max_path_length_allowed, param):
- paths = []
- if start[1] == 'L':
- forbidden = set()
- forbidden.add((start[0], 'R'))
- else:
- forbidden = set()
- forbidden.add((start[0], 'L'))
-
- path = [start]
- #Joining within scaffolds
- if is_withing_scaf:
- element = end.pop()
- end.add(element)
- if element[1] == 'L':
- forbidden.add((element[0], 'R'))
- else:
- forbidden.add((element[0], 'L'))
-
-
- #TODO: Have length criteria that limits the path lenght due to complecity reasons. Can also identify strange
- #links by looking how many neighbors a contig has and how mych the library actually can span
- queue = [path]#, sum_path)]
- #prev_node = start
- counter = 0
- while queue:
- counter += 1
- if counter > param.path_threshold or len(path) > 100:
- print 'Hit path_threshold of {0} iterations! consider increase --iter <int> parameter to over {0} if speed of BESST is not a problem. Standard increase is, e.g., 2-10x of current value'.format(param.path_threshold)
- break
-
- path = queue.pop()
- prev_node = path[-1]
-
- if len(path) > 1 and prev_node in already_visited or prev_node in forbidden:
- continue
-
- if len(path) > 1 and path[-2] in end:
- path.pop()
- paths.append(path)
- continue
-
-
- # if prev_node[1] == 'L' and (prev_node[0], 'R') not in forbidden:
- # path.append( (prev_node[0], 'R') )
- # #queue.append(path)
- # elif prev_node[1] == 'R' and (prev_node[0], 'L') not in forbidden:
- # path.append( (prev_node[0], 'L') )
- # #queue.append(path)
-
- for node in set(graph[prev_node]).difference(path):
- if node not in forbidden: # and node not in already_visited:
- new_path = path + [node]
- # path.append(node)
- if node[1] == 'L':
- new_path.append( (node[0], 'R') )
- else:
- new_path.append( (node[0], 'L') )
-
- queue.append(new_path)
-
- return paths
-
-def find_all_paths_for_start_node_DFS(graph, start, end, already_visited, is_withing_scaf, max_path_length_allowed, param):
- path = []
- paths = []
- if start[1] == 'L':
- forbidden = set()
- forbidden.add((start[0], 'R'))
- else:
- forbidden = set()
- forbidden.add((start[0], 'L'))
-
- #Joining within scaffolds
- if is_withing_scaf:
- element = end.pop()
- end.add(element)
- if element[1] == 'L':
- forbidden.add((element[0], 'R'))
- else:
- forbidden.add((element[0], 'L'))
-
-
- #TODO: Have length criteria that limits the path lenght due to complecity reasons. Can also identify strange
- #links by looking how many neighbors a contig has and how mych the library actually can span
- heap = [(0,(start, path))]#, sum_path)]
- #prev_node = start
- counter = 0
- while heap:
- #prev_node = start
- counter += 1
- #if counter % 100 == 0:
- # print 'Potential paths:', counter, 'paths found: ', len(paths)
- if counter > param.path_threshold or len(path) > 100:
- print 'Hit path_threshold of {0} iterations! consider increase --iter <int> parameter to over {0} if speed of BESST is not a problem. Standard increase is, e.g., 2-10x of current value'.format(param.path_threshold)
- break
-
- nr_links, (start, path) = heapq.heappop(heap) #start, end, path, sum_path = heapq.pop()
- try:
- prev_node = path[-1]
- except IndexError:
- prev_node = start
- path = path + [start]
- path_len = len(path)
- #print 'PATH', path ,'end', end
- if path_len > max_path_length_allowed: #All possible paths can be exponential!! need something to stop algorithm in time
- continue
- #if score < score_best_path: # need something to stop a bad path
- # continue
- if start in already_visited or start in forbidden:
- continue
-
- if start in end:
- # if (start_node, start) in nodes_present_in_path:
- # nodes_present_in_path[(start_node, start)] = nodes_present_in_path[(start_node, start)].union(path)
- # else:
- # nodes_present_in_path[(start_node, start)] = set(path)
- paths.append(path)
- continue
-
-
- if prev_node[0] != start[0]:
- nr_links = 2**16 # large number to give high priority to this intra-contig edge in this two node representation
- if start[1] == 'L' and (start[0], 'R') not in forbidden:
- heapq.heappush(heap, (nr_links, ((start[0], 'R'), path))) #, sum_path + graph[start][(start[0], 'R')]['nr_links']))
- elif start[1] == 'R' and (start[0], 'L') not in forbidden:
- heapq.heappush(heap, (nr_links, ((start[0], 'L'), path)))#, sum_path + graph[start][(start[0], 'L')]['nr_links']))
- else:
- for node in set(graph[start]).difference(path):
- if node not in forbidden: # and node not in already_visited:
- # try: # if last node (i.e. "end") it is not present in small_scaffolds and it should not be included in the length
- # heapq.heappush(heap, (nr_links, node, path, path_len + graph[node[0]]['length'])) # small_scaffolds[node[0]].s_length)) #
- # except KeyError:
- nr_links = graph[start][node]['nr_links']
- heapq.heappush(heap, (nr_links, (node, path)))
-
- return paths
-
-
-def BetweenScaffolds(G_prime, end, iter_nodes, param):
- # here we should have a for loop looping over all start nodes. Start nodes already examined should be removed in a nice way to skip over counting
- already_visited = set()
- all_paths = []
- print 'Entering "find_all_paths_for_start_node" '
- iter_count = 0
- cnter = 0
- if param.max_extensions:
- iter_threshold = param.max_extensions
- else:
- iter_threshold = len(end)
-
- print 'iterating until maximum of {0} extensions.'.format(iter_threshold)
- print 'nodes:{0}, edges: {1}'.format(len(G_prime.nodes()), len(G_prime.edges()))
- while len(iter_nodes) > 0 and iter_count <= iter_threshold:
- iter_count += 1
- start_node = iter_nodes.pop()
- if cnter % 100 == 0:
- print 'enter Betwween scaf node: ', cnter
- end.difference_update(set([start_node]))
- if param.bfs_traversal:
- #paths = find_all_paths_for_start_node_BFS(G_prime, start_node, end, already_visited, 0, 2 ** 32, param)
- paths = find_all_paths_for_start_node_BFS_improved(G_prime, start_node, end, already_visited, 0, 2 ** 32, param)
- #paths = map(lambda x: x[0], paths)
- # print 'NEW PATHS', paths2
- # print
- # print
- # print "OLD PATHS", p
- #print len(paths)
- #print len(p)
- #assert p == paths2
- else:
- paths = find_all_paths_for_start_node_DFS(G_prime, start_node, end, already_visited, 0, 2 ** 32, param)
-
- already_visited.add(start_node)
- ScorePaths(G_prime, paths, all_paths, param)
- cnter += 1
- #all_paths = ExtendScaffolds(all_paths)
- #print all_paths
- print 'Total nr of paths found: {0} with score larger than: {1}'.format(len(all_paths), param.score_cutoff)
- all_paths.sort(key=lambda list_: list_[0])
- #print all_paths
- return(all_paths)
-
-def WithinScaffolds(G, G_prime, start, end_node, already_visited, max_path_length, param):
- end = set()
- end.add(end_node)
- all_paths = []
- already_visited.difference_update(set([start, end_node]))
- if param.bfs_traversal:
- paths = find_all_paths_for_start_node_BFS(G_prime, start, end, already_visited, 1, max_path_length, param)
- else:
- paths = find_all_paths_for_start_node_DFS(G_prime, start, end, already_visited, 1, max_path_length, param)
-
- already_visited.add(start)
- already_visited.add(end_node)
- #print paths
- if len(paths) > 1:
- ScorePaths(G_prime, paths, all_paths,param)
- all_paths.sort(key=lambda list_: list_[0])
-
- if len(all_paths) > 0:
- return all_paths
-
- return []
-
-if __name__ == '__main__':
- import Scaffold
- small_scaffolds_test = {}
- for i in range(1, 7):
- S = Scaffold.scaffold(i, 0, 0, {}, {})
- small_scaffolds_test[S.name] = S
- start = time()
- G_prime = nx.Graph()
- #G.add_nodes_from([(1, 'L'), (1, 'R'), (2, 'L'), (2, 'R'), (3, 'L'), (3, 'R'), (4, 'L'), (4, 'R'), (5, 'L'), (5, 'R')])
- for i in range(1, 7):
- G_prime.add_edge((i, 'L'), (i, 'R'), {'nr_links':0})
- G_prime.add_edges_from([((1, 'R'), (2, 'R'), {'nr_links':1}), ((3, 'L'), (4, 'L'), {'nr_links':1}), ((2, 'L'), (3, 'R'), {'nr_links':1}), ((1, 'R'), (5, 'L'), {'nr_links':2}),
- ((5, 'R'), (4, 'L'), {'nr_links':3}), ((2, 'L'), (5, 'L'), {'nr_links':2}), ((1, 'R'), (4, 'L'), {'nr_links':8}), ((2, 'L'), (6, 'L'), {'nr_links':3}),
- ((1, 'L'), (4, 'R'), {'nr_links':1}), ((1, 'L'), (4, 'L'), {'nr_links':1}), ((3, 'L'), (4, 'R'), {'nr_links':1}),
- ((1, 'R'), (2, 'L'), {'nr_links':1}), ((1, 'R'), (5, 'R'), {'nr_links':1}), ((2, 'L'), (5, 'R'), {'nr_links':1})])
- G = nx.Graph()
- G.add_nodes_from([(1, 'L'), (1, 'R'), (4, 'L'), (4, 'R'), (6, 'L'), (6, 'R')])
- contigs = [1, 2, 3, 4, 5, 6]
-
- print 'Between'
- BetweenScaffolds(G, G_prime, small_scaffolds_test)
- start_node = (1, 'R')
- end_node = (4, 'L')
- print 'Within'
- already_visited = set(G.nodes())
- print already_visited
- WithinScaffolds(G, G_prime, small_scaffolds_test, start_node, end_node, already_visited, 0)
- elapsed = time() - start
- print 'time all paths: ', elapsed
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/GenerateOutput.py b/external/gatb-minia-pipeline/BESST/BESST/GenerateOutput.py
deleted file mode 100644
index 70c0f0e02aa775c0d29244f046283e80a11eb058..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/GenerateOutput.py
+++ /dev/null
@@ -1,178 +0,0 @@
-'''
- Created on Sep 29, 2011
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-rev_nuc = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'a':'t', 'c':'g', 'g':'c', 't':'a', 'N':'N', 'X':'X', 'n':'n', 'Y':'R', 'R':'Y', 'K':'M', 'M':'K', 'S':'S', 'W':'W', 'B':'V', 'V':'B', 'H':'D', 'D':'H', 'y':'r', 'r':'y', 'k':'m', 'm':'k', 's':'s', 'w':'w', 'b':'v', 'v':'b', 'h':'d', 'd':'h'}
-
-
-def longest_kmer_overlap(s1, s2):
- i = len(s1)
- while i > 0:
- if s1[-i:] == s2[:i]:
- return i
- i -= 1
- return i
-
-def PrintOutHaplotypes(Haplotypes, Contigs, output_dest):
- haplotype_file = open(output_dest + '/haplotypes.fa', 'a')
- for cont_hapl in Haplotypes:
- print >> haplotype_file, '>' + Haplotypes[cont_hapl][0] + ' (variant of ' + cont_hapl + ')'
- hapl_contig = Contigs[Haplotypes[cont_hapl][0]].sequence
- for i in range(0, len(hapl_contig), 60):
- print >> haplotype_file, hapl_contig[i:i + 60]
- #remove the output haplotype, the other one is left in graph
- del Contigs[Haplotypes[cont_hapl][0]]
- return(Contigs)
-
-def PrintOutRepeats(Repeats, Contigs, output_dest, small_contigs):
- repeat_file = open(output_dest + '/repeats.fa', 'w')
- for cont_obj in Repeats:
- print >> repeat_file, '>' + cont_obj.name
- repeat_contig = cont_obj.sequence
- for i in range(0, len(repeat_contig), 60):
- print >> repeat_file, repeat_contig[i:i + 60]
- try:
- del Contigs[cont_obj.name]
- except KeyError:
- del small_contigs[cont_obj.name]
- return()
-
-def ChangeToSmallContigs(Contigs, list_of_contigs, small_contigs):
- #change from Contigs to small_contige (contigs are included in scaffolds that does not meet the lenght criteria, they will be used in path extension algorithm)
- for cont_obj in list_of_contigs:
- del Contigs[cont_obj.name]
- small_contigs[cont_obj.name] = cont_obj
- return()
-
-def WriteToF(F, Contigs, list_of_contigs):
- info_list = []
- for cont_obj in list_of_contigs:
- info_list.append((cont_obj.name, cont_obj.direction, cont_obj.position, cont_obj.length, cont_obj.sequence)) #,cont_obj.links
- if cont_obj.position < 0:
- print 'Write to F: Position is negative!', cont_obj.position, cont_obj.name, cont_obj.direction
- #del Contigs[cont_obj.name]
- F.append(info_list)
- return(F)
-
-class Scaffold(object):
- """docstring for Scaffold"""
- def __init__(self, name, param, info_tuple):
- super(Scaffold, self).__init__()
- self.name = name
- self.param = param
-
- self.seqs = map(lambda x: x[4], info_tuple)
- self.gaps = map(lambda x,y : y[2] - (x[2] + x[3]), info_tuple[:-1],info_tuple[1:])
- self.directions = map(lambda x: x[1], info_tuple)
- self.positions = map(lambda x: (x[2],x[2] + x[3] - 1) , info_tuple)
- self.contigs = map(lambda x: x[0], info_tuple)
-
- def check_kmer_overlap(self,end1,end2):
- i = len(end1)
- while i > 0:
- if end1[-i:] == end2[:i]:
- return i
- i -= 1
- return i
-
- def get_sequence(self, string, direction):
- if direction:
- return string
- else:
- return RevComp(string,rev_nuc)
-
-
- def make_fasta_string(self,fasta_file,k_mer_overlap=200):
- fasta = []
- #fasta.append('>{0}\n'.format(self.name))
- fasta.append('>'+str(self.name)+'\n')
- # first contig
-
- fasta.append( self.get_sequence(self.seqs[0], self.directions[0]))
-
- for i in range(len(self.seqs)-1):
- gap = self.gaps[i]
- if gap <= 2*self.param.std_dev_ins_size:
- overlap = self.check_kmer_overlap( self.get_sequence(self.seqs[i], self.directions[i])[-k_mer_overlap:], self.get_sequence(self.seqs[i+1], self.directions[i+1])[:k_mer_overlap])
- if overlap >= 20:
- fasta.append('n' + self.get_sequence(self.seqs[i+1], self.directions[i+1])[overlap:])
- print 'merging {0} bp here'.format(overlap)
- else:
- #print gap
- if gap <= 1:
- fasta.append('n' + self.get_sequence(self.seqs[i+1], self.directions[i+1]))
- else:
- fasta.append('N'*int(gap) + self.get_sequence(self.seqs[i+1], self.directions[i+1]))
- else:
- if gap <= 1:
- fasta.append('n' + self.get_sequence(self.seqs[i+1], self.directions[i+1]))
- else:
- fasta.append('N'*int(gap) + self.get_sequence(self.seqs[i+1], self.directions[i+1]))
-
-
- print >> fasta_file, ''.join([ x for x in fasta])
-
- def make_AGP_string(self, AGP_file):
- component_count = 0
- for i in range(len(self.seqs)-1):
- sign = '+' if self.directions[i] else '-'
- if i > 0 and self.gaps[i-1] > 0:
- component_count += 1
- print >> AGP_file, self.name + '\t' + str(self.positions[i-1][1] + 1) + '\t' + str(self.positions[i][0]-1) + '\t' + str(component_count) + '\t' + 'N\t' + str(self.gaps[i]) + '\tfragment\tyes\t'
- component_count += 1
- print >> AGP_file, self.name + '\t' + str(self.positions[i][0]) + '\t' + str(self.positions[i][1]) + '\t' + str(component_count) + '\t' + 'W\t' + self.contigs[i] + '\t1\t' + str(self.positions[i][1] - self.positions[i][0] + 1) + '\t' + sign
-
-
-def PrintOutput(F, Information, output_dest, param, pass_nr):
- import os
- try:
- os.mkdir(param.output_directory + '/pass' + str(pass_nr))
- except OSError:
- #directory is already created
- pass
- #contigs_before=len(C_dict)
- contigs_after = len(F)
- print >> Information, '(super)Contigs after scaffolding: ' + str(contigs_after) + '\n'
- gff_file = open(param.output_directory + '/pass' + str(pass_nr) + '/info-pass' + str(pass_nr) + '.gff', 'w')
- AGP_file = open(param.output_directory + '/pass' + str(pass_nr) + '/info-pass' + str(pass_nr) + '.agp', 'w')
- print >> gff_file, '#gff-version 3'
- print >> AGP_file, '#APG file\n#lw-scaffolder output'
- fasta_file = open(param.output_directory + '/pass' + str(pass_nr) + '/Scaffolds-pass' + str(pass_nr) + '.fa', 'w')
- header_index = 0
-
- for scaf_ in reversed(F):
- #sort contigs in scaf w.r.t position here
- scaf = sorted(scaf_, key=lambda tuple: tuple[2])
- header_index += 1
-
-
- s = Scaffold('scaffold_' + str(header_index), param, scaf)
- s.make_fasta_string(fasta_file)
- s.make_AGP_string(AGP_file)
-
- return()
-
-
-def RevComp(string, rev_nuc):
- #rev_nuc={'A':'T','C':'G','G':'C','T':'A','N':'N','X':'X'}
- rev_comp = ''.join([rev_nuc[nucl] for nucl in reversed(string)])
- return(rev_comp)
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/MakeScaffolds.py b/external/gatb-minia-pipeline/BESST/BESST/MakeScaffolds.py
deleted file mode 100644
index 5e19288d100b217e0d5fcaedea3cc092e71f44fd..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/MakeScaffolds.py
+++ /dev/null
@@ -1,1706 +0,0 @@
-'''
- Created on Sep 29, 2011
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-import sys
-from collections import defaultdict
-import time
-import copy
-
-import networkx as nx
-from networkx import algorithms
-import multiprocessing
-
-import Contig, Scaffold, Parameter
-import GenerateOutput as GO
-from mathstats.normaldist.truncatedskewed import param_est as GC
-import mathstats.log_normal_param_est as lnpe
-from mathstats.normaldist import normal
-import ExtendLargeScaffolds as ELS
-import haplotypes as HR
-import plots
-import order_contigs
-
-
-# def constant_large():
-# return 2 ** 32
-
-# def constant_small():
-# return -1
-
-
-def Algorithm(G, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, Information, param):
- #search for linear streches in the graph, remove all cliques >2 and all contigs having more than three neighbors
- nr_edges = 0
- for edge in G.edges_iter():
- if G[edge[0]][edge[1]]['nr_links']:
- nr_edges += 1
-
- print >> Information, str(nr_edges) + ' link edges created.'
- print >> Information, 'Perform inference on scaffold graph...'
-
- #VizualizeGraph(G,param,Information)
-
- if param.detect_haplotype:
- HR.HaplotypicRegions(G, G_prime, Contigs, Scaffolds, param, Information)
- #save graph in dot format to file here
-
- ##If sigma specified. Pre calculate a look up table for every possible gap estimate in the common case
- ##where we have two long contigs that are linked. We do this one time per library to save computation time.
- if param.std_dev_ins_size:
- dValuesTable = GC.PreCalcMLvaluesOfdLongContigs(param.mean_ins_size, param.std_dev_ins_size, param.read_len)
- else :
- dValuesTable = None
- already_visited = set()
- if param.extend_paths:
- for node in G:
- already_visited.add(node)
-
-
- ##### Here is the scaffolding algorithm #######
-
- G = RemoveIsolatedContigs(G, Information) #step1
- plot = 'G'
-
- if not param.no_score:
- RemoveAmbiguousRegionsUsingScore(G, G_prime, Information, param, plot) #step2
- G = RemoveIsolatedContigs(G, Information) #there are probably new isolated nodes created from step 2
- G, Contigs, Scaffolds = RemoveLoops(G, G_prime, Scaffolds, Contigs, Information, param) #step4
- #The contigs that made it to proper scaffolds
- (Contigs, Scaffolds, param) = NewContigsScaffolds(G, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, Information, dValuesTable, param, already_visited) #step5
- ##Here PathExtension algorithm between created scaffolds is called if PRO is activated
-
- if param.extend_paths:
- print >> Information, '\n\n\n Searching for paths BETWEEN scaffolds\n\n\n'
- PROBetweenScaf(G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, param, dValuesTable, Information)
- print >> Information, 'Nr of contigs left: ', len(G_prime.nodes()) / 2.0, 'Nr of linking edges left:', len(G_prime.edges()) - len(G_prime.nodes()) / 2.0
- print >> Information, 'Number of gaps estimated by GapEst-LP module order_contigs in this step is: {0}'.format(param.path_gaps_estimated)
-
- if param.plots:
- if len(param.gap_estimations) > 0:
- plots.histogram(param.gap_estimations, param, bins=50, x_label='gap size', y_label='Frequency', title='GapPredictions', nr_obs = len(param.gap_estimations))
-
- ## TODO: Look if we can use the new pathgaps theory to include these isolated
- ## regions of small contigs in the scaffolding
-
-#
-# for node in G_prime.nodes():
-# nbrs = G_prime.neighbors(node)
-# for nbr in nbrs:
-# if G_prime[node][nbr]['nr_links'] and 'score' not in G_prime[node][nbr]:
-# G_prime.remove_edge(node, nbr)
-#
-# plot = 'G_prime'
-# #print 'GOING IN:', len(G_prime.edges()), len(G_prime.nodes())
-# RemoveAmbiguousRegionsUsingScore(G_prime, G_prime, Information, param, plot)
-# G_prime, Contigs, Scaffolds = RemoveLoops(G_prime, G_prime, Scaffolds, Contigs, Information, param)
-# for node in G_prime:
-# if node[0] not in Scaffolds:
-# scaf_obj = small_scaffolds[node[0]]
-# Scaffolds[node[0]] = scaf_obj
-# cont_objects = scaf_obj.contigs
-# for obj_ in cont_objects:
-# ctg_name = obj_.name
-# Contigs[ctg_name] = obj_
-# del small_contigs[ctg_name]
-# del small_scaffolds[node[0]]
-# (Contigs, Scaffolds, param) = NewContigsScaffolds(G_prime, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, Information, dValuesTable, param, already_visited)
-
-
- ####### End of algorithm #####################
-
-
- return()
-
-
-
-def RemoveIsolatedContigs(G, Information):
- print >> Information, 'Remove isolated nodes.'
- counter = 0
- for node in G.nodes():
- if node in G:
- nbr = G.neighbors(node)[0]
- if len(G.neighbors(node)) == 1 and len(G.neighbors(nbr)) == 1:
- counter += 1
- G.remove_nodes_from([node, nbr])
- print >> Information, str(counter) + ' isolated contigs removed from graph.'
- return(G)
-
-
-def partition(pred, iterable):
- trues = []
- falses = []
- for item in iterable:
- if pred(item):
- trues.append(item)
- else:
- falses.append(item)
- return trues, falses
-
-def remove_edges(G, G_prime, Information, param, node, score_chosen_obs, non_zero_score_removed_obs, edge_score_to_zero, record_decision):
- nbrs = G.neighbors(node)
-
-
- #Remove ambiguous edges
- filter_nbrs = filter(lambda nbr: 0 < G[node][nbr]['nr_links'] , nbrs) # remove other side of contig (has no "links")
- score_list_temp = sorted(map(lambda nbr: (G[node][nbr]['score'], nbr), filter_nbrs)) # sort list of scores for neighbors
- non_zero_score_edges, zero_score_edges = partition(lambda nbr: 0 < G[node][nbr[1]]['score'], score_list_temp) # Split list into 0-scoring and non-0-scoring edges
-
-
- #remove all zero score edges
- remove_zero_score_edges = map(lambda item: (node, item[1]) , zero_score_edges)
- G.remove_edges_from(remove_zero_score_edges)
- if param.plots:
- for item in zero_score_edges:
- edge_score_to_zero.append(item[0])
-
- if param.extend_paths:
- try: #we might have been removed this edge from G_prime when we did individual filtering of G_prime in CreateGraph module
- G_prime.remove_edges_from(remove_zero_score_edges)
- except nx.exception.NetworkXError:
- pass
-
- # Remove lower non zero score edges
- if len(non_zero_score_edges) > 1:
- if non_zero_score_edges[-2][0] / non_zero_score_edges[-1][0] > 0.9:
- print >> Information, 'SCORES AMBVIVALENT', non_zero_score_edges[-1][0], non_zero_score_edges[-2][0]
- remove_non_zero_edges = map(lambda item: (node, item[1]) , non_zero_score_edges) # Edges that does not have a score of 0 but are not the highest scoring one in an ambigous region
- else:
- remove_non_zero_edges = map(lambda item: (node, item[1]) , non_zero_score_edges[:-1]) # Edges that does not have a score of 0 but are not the highest scoring one in an ambigous region
-
- G.remove_edges_from(remove_non_zero_edges) # remove the lower scoring edges
- if param.extend_paths:
- try: #we might have been removed this edge from G_prime when we did individual filtering of G_prime in CreateGraph module
- G_prime.remove_edges_from(remove_non_zero_edges)
- except nx.exception.NetworkXError:
- pass
-
- if param.plots:
- if len(non_zero_score_edges) > 0:
- if record_decision:
- score_chosen_obs.append(non_zero_score_edges[-1][0])
- for item in non_zero_score_edges[:-1]:
- non_zero_score_removed_obs.append(item[0])
-
-
- return()
-
-def RemoveAmbiguousRegionsUsingScore(G, G_prime, Information, param, plot):
- score_chosen_obs = []
- non_zero_score_removed_obs = []
- edge_score_to_zero = []
-
- nr_edges_before = len(G.edges())
- print >> Information, 'Remove edges from node if more than two edges'
- #counter1 = 0
-
- link_edges = filter(lambda x: 'score' in x[2], G.edges(data=True))
- edge_scores_sorted = sorted(link_edges, key=lambda x: x[2]['score'], reverse=True)
-
- for edge in edge_scores_sorted:
- remove_edges(G, G_prime, Information, param, edge[0], score_chosen_obs, non_zero_score_removed_obs, edge_score_to_zero, True)
- remove_edges(G, G_prime, Information, param, edge[1], score_chosen_obs, non_zero_score_removed_obs, edge_score_to_zero, False)
-
- nr_edges_after = len(G.edges())
- #print >> Information, str(counter1) + ' ambiguous regions in graph ( a contig with more than 2 neighbors).'
- print >> Information, ' Number of edges in G before:', nr_edges_before
- print >> Information, ' Number of edges in G after:', nr_edges_after
- try:
- print >> Information, ' %-age removed edges:', 100 * (1 - (nr_edges_after / float(nr_edges_before)))
- except ZeroDivisionError:
- pass
-
- if param.plots:
- print len(score_chosen_obs)
- list_of_datasets = [edge_score_to_zero, score_chosen_obs , non_zero_score_removed_obs]
- plots.multiple_histogram(list_of_datasets, param, 'score', 'frequency', title='Besst_decision_scores' + plot + '.' + param.bamfile.split('/')[-1])
-
- return()
-
-
-
-
-
-
-def RemoveLoops(G, G_prime, Scaffolds, Contigs, Information, param):
-#### After the proceure above, we hope that the graph is almost perfectly linear but we can still be encountering cycles (because of repeats or haplotypic contigs that has slipped through our conditions). Thus we finally search for loops
- print >> Information, 'Contigs/scaffolds left:', len(G.nodes()) / 2
- print >> Information, 'Remove remaining cycles...'
- #graphs = nx.connected_component_subgraphs(G)
- #print 'Nr connected components',len(graphs)
- counter = 0
- #for graph in graphs:
- list_of_cycles = algorithms.cycles.cycle_basis(G)
- for cycle in list_of_cycles:
- print >> Information, 'A cycle in the scaffold graph: ' + str(cycle) + '\n'
- print >> Information, 'A cycle in the scaffold graph: ' + str(cycle)
- counter += 1
- for node in cycle:
- if node in G:
- #we split up the whole cycle into separate contigs and send them to F
- scaffold_ = node[0]
- G.remove_nodes_from([(scaffold_, 'L'), (scaffold_, 'R')])
- if param.extend_paths:
- G_prime.remove_nodes_from([(scaffold_, 'L'), (scaffold_, 'R')])
-# S_obj=Scaffolds[scaffold_]
-# list_of_contigs=S_obj.contigs #list of contig objects contained in scaffold object
-# Contigs, F = GO.WriteToF(F,Contigs,list_of_contigs)
-# del Scaffolds[scaffold_]
- print >> Information, str(counter) + ' cycles removed from graph.'
- return(G, Contigs, Scaffolds)
-
-
-def NewContigsScaffolds(G, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, Information, dValuesTable, param, already_visited):
-### Remaining scaffolds are true sensible scaffolds, we must now update both the library of scaffold objects and the library of contig objects
- new_scaffolds_ = [ G.subgraph(c) for c in nx.connected_components(G)]
- #print 'INITIAL SCAFFOLD INDEX:',param.scaffold_indexer
- print >> Information, 'Nr of new scaffolds created in this step: ' + str(len(new_scaffolds_))
- for new_scaffold_ in new_scaffolds_:
- param.scaffold_indexer += 1
- #scaf_size=len(new_scaffold_)
- scaffold_length = 0
- contig_list = []
-
- ##### Here PathExtension algorithm is called if PRO is activated #####
- if param.extend_paths:
- #print 'SCAFFOLD INDEX:',param.scaffold_indexer
- PROWithinScaf(G, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, param, new_scaffold_, dValuesTable, already_visited)
-
- for node in new_scaffold_:
- if len(G.neighbors(node)) == 1:
- start = node
- break
- for node in new_scaffold_:
- if len(G.neighbors(node)) == 1 and node != start:
- end = node
- #Create info to new scaffold object such as total length and the contig objects included
-
- prev_node = ('', '')
- pos = 0
- values = UpdateInfo(G, Contigs, small_contigs, Scaffolds, small_scaffolds, start, prev_node, pos, contig_list, scaffold_length, dValuesTable, param)
- #print values
- while len(values) !=2:
- values = UpdateInfo(G,*values)
- #print len(values)
- #(G, contig_list, scaffold_length) = UpdateInfo(G, Contigs, small_contigs, Scaffolds, small_scaffolds, start, prev_node, pos, contig_list, scaffold_length, dValuesTable, param)
- contig_list, scaffold_length = values[0],values[1]
- S = Scaffold.scaffold(param.scaffold_indexer, contig_list, scaffold_length) #Create the new scaffold object
-
- Scaffolds[S.name] = S #include in scaffold library
-
- if param.extend_paths:
- # Find the ends of the old subgraph new_scaffold_. We want them to be able to relabel these end nodes as the new sides on the new scaffold object created
- #only these ends are allowed to have links because they are of size mean+ 4*sigma so nothing is supposed to span over.
-
- #add the new scaffold object to G_prime
-
- G_prime.add_node((S.name, 'L')) #start node
- G_prime.add_node((S.name, 'R')) # end node
- G_prime.add_edge((S.name, 'L'), (S.name, 'R'), nr_links=None)
- try:
- for nbr in G_prime.neighbors(start):
- nr_links_ = G_prime[start][nbr]['nr_links']
- if nr_links_:
- obs_ = G_prime[start][nbr]['obs']
- observations_ = G_prime[start][nbr]['observations']
- # G_prime.add_edge((S.name, 'L'), nbr, nr_links=nr_links_, obs=obs_)
- obs_sq_ = G_prime[start][nbr]['obs_sq']
- G_prime.add_edge((S.name, 'L'), nbr, nr_links=nr_links_, obs=obs_, obs_sq=obs_sq_, observations=observations_)
-
- for nbr in G_prime.neighbors(end):
- nr_links_ = G_prime[end][nbr]['nr_links']
- if nr_links_:
- obs_ = G_prime[end][nbr]['obs']
- observations_ = G_prime[end][nbr]['observations']
- # G_prime.add_edge((S.name, 'R'), nbr, nr_links=nr_links_, obs=obs_)
- obs_sq_ = G_prime[end][nbr]['obs_sq']
- G_prime.add_edge((S.name, 'R'), nbr, nr_links=nr_links_, obs=obs_, obs_sq=obs_sq_, observations=observations_)
-
- #remove the old scaffold objects from G_prime
- G_prime.remove_nodes_from(new_scaffold_)
- except nx.exception.NetworkXError:
- pass
-
- return(Contigs, Scaffolds, param)
-
-
-def UpdateInfo(G, Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param):
- scaf = node[0]
- side = node[1]
- prev_scaf = prev_node[0]
- if len(G.neighbors((scaf, side))) == 0: #reached end of scaffol
- #find the contig with the largest position
- object_with_largest_pos_in_scaffold = max(contig_list, key=lambda object: object.position + object.length)
- scaffold_length = object_with_largest_pos_in_scaffold.position + object_with_largest_pos_in_scaffold.length
-# try:
- del Scaffolds[scaf] #finally, delete the old scaffold object
- G.remove_node((scaf, side))
-# except KeyError:
-# del small_scaffolds[scaf] #finally, delete the old scaffold object
- return(contig_list, scaffold_length)
- else:
- nbr_node = G.neighbors((scaf, side))
- nbr_scaf = nbr_node[0][0]
- nbr_side = nbr_node[0][1]
- if scaf != prev_scaf:
- if side == 'L': #Contig/scaffold still has same orientation as in previous iteration, just update position in scaffold
- #want to assign nr of links to contig object, note that in case of a "multiple contigs"-scaffold object, only the outermost contig holds the information of the total nr of links between the two scaffold objects
- #try:
- contig_objects = Scaffolds[scaf].contigs #list of contig objects
- #except KeyError:
- # contig_objects=small_scaffolds[scaf].contigs #list of contig objects
- #Update just update position in scaffold
- for contig in contig_objects:
- contig.scaffold = param.scaffold_indexer
- contig.position += pos
- #direction unchanged
- contig_list.append(contig)
- G.remove_node((scaf, side))
- prev_node = node
- node = (nbr_scaf, nbr_side)
- #try:
- pos += Scaffolds[scaf].s_length #update position before sending it to next scaffold
- #except KeyError:
- # pos+=small_scaffolds[scaf].s_length #update position before sending it to next scaffold
-
- return Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param
-
- #G, contig_list, scaffold_length = UpdateInfo(G, Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param)
-
- else: #Contig/scaffold need to change orientation as well as modify orientation in this case
- #try:
- contig_objects = Scaffolds[scaf].contigs #list of contig objects
- #except KeyError:
- # contig_objects=small_scaffolds[scaf].contigs #list of contig objects
-
- for contig in contig_objects:
- contig.scaffold = param.scaffold_indexer
- #try:
- curr_scaf_length = Scaffolds[scaf].s_length
- #except KeyError:
- # curr_scaf_length=small_scaffolds[scaf].s_length
-
- curr_pos_within_scaf = contig.position
- contig_length = contig.length
- contig.position = pos + (curr_scaf_length - curr_pos_within_scaf) - contig_length #updates the position within scaf
- contig.direction = bool(True -contig.direction) #changes the direction
- contig_list.append(contig)
-
- G.remove_node((scaf, side))
- prev_node = node
- node = (nbr_scaf, nbr_side)
- #try:
- pos += Scaffolds[scaf].s_length #update position before sending it to next scaffold
- #except KeyError:
- #pos+=small_scaffolds[scaf].s_length #update position before sending it to next scaffold
-
- return Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param
-
-# G, contig_list, scaffold_length = UpdateInfo(G, Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param)
- else:
- if 'avg_gap' not in G[(scaf, side)][(nbr_scaf, nbr_side)]:
- #calculate gap to next scaffold
- c1_len = Scaffolds[scaf].s_length
- c2_len = Scaffolds[nbr_scaf].s_length
- if param.lognormal:
- print G[(scaf, side)][(nbr_scaf, nbr_side)]
- print G[(scaf, side)]
- samples = G[(scaf, side)][(nbr_scaf, nbr_side)]['observations']
- avg_gap = lnpe.GapEstimator(param.lognormal_mean, param.lognormal_sigma, param.read_len, samples, c1_len, c2_len=c2_len)
- else:
-
- sum_obs = G[(scaf, side)][(nbr_scaf, nbr_side)]['obs']
- nr_links = G[(scaf, side)][(nbr_scaf, nbr_side)]['nr_links']
- data_observation = (nr_links * param.mean_ins_size - sum_obs) / float(nr_links)
- mean_obs = sum_obs / float(nr_links)
- #try:
- c1_len = Scaffolds[scaf].s_length
- #except KeyError:
- # c1_len=small_scaffolds[scaf].s_length
- #try:
- c2_len = Scaffolds[nbr_scaf].s_length
- #except KeyError:
- # c2_len=small_scaffolds[nbr_scaf].s_length
- #do fancy gap estimation by the bias estimator formula
- if param.std_dev_ins_size and nr_links >= 5:
- #pre calculated value in lookup table
- if c1_len > param.mean_ins_size + 4 * param.std_dev_ins_size and c2_len > param.mean_ins_size + 4 * param.std_dev_ins_size:
- #(heuristic scale down of table to gaps of at most 2 stddevs away from mean)
- try:
- avg_gap = dValuesTable[int(round(data_observation, 0))]
- except KeyError:
- avg_gap = GC.GapEstimator(param.mean_ins_size, param.std_dev_ins_size, param.read_len, mean_obs, c1_len, c2_len)
- #print 'Gap estimate was outside the boundary of the precalculated table, obs were: ', data_observation, 'binary search gave: ', avg_gap
- #Do binary search for ML estimate of gap if contigs is larger than 3 times the std_dev
- elif c1_len > param.std_dev_ins_size + param.read_len and c2_len > param.std_dev_ins_size + param.read_len:
- avg_gap = GC.GapEstimator(param.mean_ins_size, param.std_dev_ins_size, param.read_len, mean_obs, c1_len, c2_len)
- else:
- #print 'now', 2 * param.std_dev_ins_size + param.read_len
- avg_gap = int(data_observation)
- param.gap_estimations.append( avg_gap )
- #print 'Gapest if used:' + str(int(avg_gap)), 'Naive: ' + str(int(data_observation)), c1_len, c2_len, Scaffolds[scaf].contigs[0].name, Scaffolds[nbr_scaf].contigs[0].name
- #See if the two contigs are in fact negatively overlapped in the delta file, , then abyss produses
- #contigs contained in other contigs
- #do naive gap estimation
- else:
- avg_gap = int(data_observation)
- param.gap_estimations.append( avg_gap )
- else:
- avg_gap = G[(scaf, side)][(nbr_scaf, nbr_side)]['avg_gap']
- param.gap_estimations.append( avg_gap )
-
- if avg_gap <= 1:
- avg_gap = 1
-
- pos += int(avg_gap)
- G.remove_node((scaf, side))
- prev_node = node
- node = (nbr_scaf, nbr_side)
- #try:
- del Scaffolds[scaf] #finally, delete the old scaffold object
- #except KeyError:
- # del small_scaffolds[scaf] #finally, delete the old scaffold object
- return Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param
- #G, contig_list, scaffold_length = UpdateInfo(G, Contigs, small_contigs, Scaffolds, small_scaffolds, node, prev_node, pos, contig_list, scaffold_length, dValuesTable, param)
- return( contig_list, scaffold_length)
-
-def get_total_length(Scaffolds, small_scaffolds, path):
- total_within_path_length = 0
- for i,node in enumerate(path[1:-1]):
- if i % 2 ==0:
- try:
- total_within_path_length += small_scaffolds[node[0]].s_length
- except KeyError:
- print 'Contig/Scaffold {0} is not in small_scaffolds'.format(node[0])
- return -1
- return total_within_path_length
-
-
-
-
-
-def PROWithinScaf(G, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, param, new_scaffold_, dValuesTable, already_visited):
- #loc_count = 0
- for edge in new_scaffold_.edges_iter():
- nr_links_ = G[edge[0]][edge[1]]['nr_links']
- if nr_links_:
- start = edge[0]
- end = edge[1]
- c1_len = Scaffolds[start[0]].s_length
- c2_len = Scaffolds[end[0]].s_length
- sum_obs = G[start][end]['obs']
- data_observation = (nr_links_ * param.mean_ins_size - sum_obs) / float(nr_links_)
- #avg_gap = GC.GapEstimator(param.mean_ins_size, param.std_dev_ins_size, param.read_len, data_observation, c1_len, c2_len)
-
- #high_score_path, bad_links, score, path_len = ELS.WithinScaffolds(G, G_prime, start, end, already_visited, param.ins_size_threshold, param)
- all_paths_sorted_wrt_score = ELS.WithinScaffolds(G, G_prime, start, end, already_visited, param.ins_size_threshold, param)
-
- high_score_path = False
- for path_info in reversed(all_paths_sorted_wrt_score):
- path = path_info[2]
- length_of_path = get_total_length(Scaffolds, small_scaffolds, path)
- if 0 < length_of_path < param.ins_size_threshold:
- high_score_path, score = path, path_info[0]
- break
- if not all_paths_sorted_wrt_score:
- continue
-
- # if all_paths_sorted_wrt_score[-1][1] != 0:
- # sublist = all_paths_sorted_wrt_score[-1]
- # bad_links = sublist[1]
- # score = sublist[0]
- # path_len = sublist[3]
- # print 'Path: path length: {0}, nr bad links: {1}, score: {2} '.format((path_len - 2) / 2.0, bad_links, score)
-
- # # for sublist in reversed(all_paths_sorted_wrt_score):
- # # path = sublist[2]
- # # bad_links = sublist[1]
- # # score = sublist[0]
- # # path_len = sublist[3]
- # # print 'Path: path length: {0}, nr bad links: {1}, score: {2} '.format((path_len - 2) / 2.0, bad_links, score)
-
- #high_score_path, score = all_paths_sorted_wrt_score[-1][2], all_paths_sorted_wrt_score[-1][0]
- #print 'Highest scoring path:{0}'.format(high_score_path)
- #print 'Score: {0}'.format(score)
-
- if high_score_path and score >= param.score_cutoff:
-
- ##################### v1.0.4.5
- ## modified improved path gap estimation here!!
-
- high_score_path_copy = copy.deepcopy(high_score_path)
- G_, path = estimate_path_gaps(Contigs, small_contigs, high_score_path_copy,Scaffolds,small_scaffolds, G_prime,param)
- del path[0]
- del path[-1]
- G.remove_edge(start, end)
- G.add_edges_from(G_.edges(data=True))
- G_prime.remove_nodes_from(path[1:-1])
-
- # also remove the edges from inner ends of the large scaffolds so they can't be
- # involved in creating paths in "between scaffolds"
-
- G_prime.remove_node(path[0])
- G_prime.remove_node(path[-1])
- if path[0][1] == 'L':
- G_prime.add_edge(path[0],(path[0][0],'R'),nr_links=None)
- else:
- G_prime.add_edge(path[0],(path[0][0],'L'),nr_links=None)
- if path[-1][1] == 'L':
- G_prime.add_edge(path[-1],(path[-1][0],'R'),nr_links=None)
- else:
- G_prime.add_edge(path[-1],(path[-1][0],'L'),nr_links=None)
-
- # move all contig and scaffold objects from "small" structure to large structure to fit with UpdateInfo structure
- small_scafs = map(lambda i: path[i], filter(lambda i: i % 2 == 1, range(len(path) - 1)))
- for item in small_scafs:
- scaf_obj = small_scaffolds[item[0]]
- Scaffolds[item[0]] = scaf_obj
- cont_objects = scaf_obj.contigs
- for obj_ in cont_objects:
- ctg_name = obj_.name
- Contigs[ctg_name] = obj_
- del small_contigs[ctg_name]
- del small_scaffolds[item[0]]
- #sys.exit()
- ######################################
-
-
-
- # #loc_count += 1
- # #remove edge in G to fill in the small scaffolds
- # G.remove_edge(start, end)
- # #add small scaffolds to G
- # for i in range(0, len(high_score_path) - 1):
- # nr_lin = G_prime[high_score_path[i]][high_score_path[i + 1]]['nr_links']
- # try:
- # total_dist = G_prime[high_score_path[i]][high_score_path[i + 1]]['obs']
- # G.add_edge(high_score_path[i], high_score_path[i + 1], nr_links=nr_lin, obs=total_dist)
- # except KeyError:
- # G.add_edge(high_score_path[i], high_score_path[i + 1], nr_links=nr_lin)
- # #remove the small contigs from G_prime
- # G_prime.remove_nodes_from(high_score_path[1:-1])
- # # move all contig and scaffold objects from "small" structure to large structure to fit with UpdateInfo structure
- # small_scafs = map(lambda i: high_score_path[i], filter(lambda i: i % 2 == 1, range(len(high_score_path) - 1)))
- # for item in small_scafs:
- # scaf_obj = small_scaffolds[item[0]]
- # Scaffolds[item[0]] = scaf_obj
- # cont_objects = scaf_obj.contigs
- # for obj_ in cont_objects:
- # ctg_name = obj_.name
- # Contigs[ctg_name] = obj_
- # del small_contigs[ctg_name]
- # del small_scaffolds[item[0]]
-
- ####################################################################
- return()
-
-
-def other_end(node):
- if node[1] == 'L':
- return (node[0],'R')
- elif node[1] == 'R':
- return (node[0],'L')
- else:
- print 'Node is not properly declared (has not right or left end)'
- sys.exit()
-
-
-
-def permute_path(path, ctg_to_move, contig_after):
- pos_ctg_to_move_left = path.index((ctg_to_move,'L'))
- pos_ctg_to_move_right = path.index((ctg_to_move,'R'))
-
- path = filter(lambda x: x[0] != ctg_to_move, path)
- pos_of_ctg_after = map(lambda x: x[0],path).index(contig_after)
- if pos_ctg_to_move_right < pos_ctg_to_move_left:
- path.insert(pos_of_ctg_after, (ctg_to_move,'L') )
- path.insert(pos_of_ctg_after, (ctg_to_move,'R') )
- else:
- path.insert(pos_of_ctg_after, (ctg_to_move,'R') )
- path.insert(pos_of_ctg_after, (ctg_to_move,'L') )
-
- return path
-
-# def permutation_ok(path,):
-
-# self.mean = param.mean_ins_size
-# self.stddev = param.std_dev_ins_size
-# self.read_len = param.read_len
-# self.contamination_ratio = param.contamination_ratio
-# self.contamination_mean = param.contamination_mean
-# self.contamination_stddev = param.contamination_stddev
-# self.ctgs = []
-# for i,length in enumerate(ctg_lengths):
-# self.ctgs.append(Contig(i, length))
-# self.ctgs = tuple(self.ctgs)
-# self.gaps = [0]*(len(ctg_lengths)-1) # n contigs has n-1 gaps between them, start with gap size 0
-
-# # get positions for when all gaps are 0
-# self.update_positions()
-
-# # let us cheat here! Instead of calculating likeliooods of thousands of
-# # onservations we calculate the ikelihood for them average (mean) of the
-# # observations and weight it with the number of observations
-# self.mp_links = 0.0
-# self.pe_links = 0.0
-# obs_dict = {}
-
-# for c1,c2,is_PE_link in observations:
-# #nr_obs = len(observations[(c1,c2,is_PE_link)])
-# mean_obs, nr_obs, stddev_obs = observations[(c1,c2,is_PE_link)]
-# if is_PE_link:
-# mean_PE_obs = self.ctgs[c1].length + self.ctgs[c2].length - observations[(c1,c2,is_PE_link)][0] + 2*param.read_len
-# #PE_obs = map(lambda x: self.ctgs[c1].length + self.ctgs[c2].length - x + 2*param.read_len ,observations[(c1,c2,is_PE_link)])
-# #mean_obs = sum( PE_obs)/nr_obs
-# obs_dict[(c1, c2, is_PE_link)] = (mean_PE_obs, nr_obs, stddev_obs)
-# self.pe_links += nr_obs
-# if mean_PE_obs > self.contamination_mean + 6 * self.contamination_stddev and not initial_path:
-# self.observations = None
-# return None
-# else:
-# #mean_obs = sum(observations[(c1,c2,is_PE_link)])/nr_obs
-# obs_dict[(c1, c2, is_PE_link)] = (mean_obs, nr_obs, stddev_obs)
-# self.mp_links += nr_obs
-
-
-
-
-def calculate_path_LP(current_path, Scaffolds, small_scaffolds, observations, param, moved_forward=None, shifted=None):
- contigs_to_indexes = {}
- indexes_to_contigs = {}
- index = 0
- #print 'CURNNNT PATH_',current_path
- for ctg in current_path:
- if ctg[0] in contigs_to_indexes:
- continue
- else:
- contigs_to_indexes[ctg[0]] = index
- indexes_to_contigs[index] = ctg[0]
-
- index += 1
-
- contig_lengths = []
- for ctg in contigs_to_indexes:
- try:
- contig_lengths.append((contigs_to_indexes[ctg], Scaffolds[ctg].s_length))
- except KeyError:
- contig_lengths.append((contigs_to_indexes[ctg], small_scaffolds[ctg].s_length))
-
- #contig_lengths2 = map(lambda x: (contigs_to_indexes[x], Scaffolds[x].s_length), contigs_to_indexes)
-
- #print contig_lengths
- ctg_lengths_index_ordered = map(lambda x: x[1], sorted(contig_lengths, key=lambda x: x[0]))
- #print ctg_lengths_index_ordered
- tot_links = 0
- mp_links = 0
- index_observations = {}
- permuted_contigs = set([moved_forward, shifted])
-
- for c1,c2 in observations:
- tot_links += observations[(c1,c2)][1]
- if current_path.index(c1) < current_path.index(c2) and current_path.index(c1) % 2 == 1 and current_path.index(c2) % 2 == 0 and param.contamination_ratio:
- PE = 1
- #print 'PE link!!',c1,c2
- elif current_path.index(c1) > current_path.index(c2) and current_path.index(c1) % 2 == 0 and current_path.index(c2) % 2 == 1 and param.contamination_ratio:
- PE = 1
- #print 'PE link!!',c1,c2
- elif current_path.index(c1) < current_path.index(c2) and current_path.index(c1) % 2 == 0 and current_path.index(c2) % 2 == 1:
- PE = 0
- mp_links += observations[(c1,c2)][1]
- #print 'MP link!!',c1,c2
- elif current_path.index(c1) > current_path.index(c2) and current_path.index(c1) % 2 == 1 and current_path.index(c2) % 2 == 0:
- mp_links += observations[(c1,c2)][1]
- PE = 0
- #print 'MP link!!',c1,c2
- else:
- PE = -1
- #print 'Spurious link!!',c1,c2
-
- if PE == -1:
- # we dont want to have a spurious link to contiribute to the LP objective value
- continue
- else:
- i1, i2 = min(contigs_to_indexes[c1[0]], contigs_to_indexes[c2[0]]), max(contigs_to_indexes[c1[0]], contigs_to_indexes[c2[0]])
- index_observations[(i1,i2,PE)] = observations[(c1,c2)]
-
- if c1[0] in permuted_contigs and c2[0] in permuted_contigs:
- index_moved_forward = i1
- index_shifted = i2
-
- if moved_forward and shifted:
- is_PE_link = 1
- mean_obs, nr_obs, stddev_obs, list_of_obs = index_observations[(index_moved_forward, index_shifted, is_PE_link)]
- mean_PE_obs = ctg_lengths_index_ordered[index_moved_forward] + ctg_lengths_index_ordered[index_shifted] - mean_obs + 2*param.read_len
- if mean_PE_obs > param.contamination_mean + 6 * param.contamination_stddev:
- #print 'permuted link invalid. Continuing..'
- if all(length in ctg_lengths_index_ordered for length in [670, 2093]) or all(length in ctg_lengths_index_ordered for length in [900, 3810]) or all(length in ctg_lengths_index_ordered for length in [2528, 591]) or all(length in ctg_lengths_index_ordered for length in [734, 257, 1548]):
- print >> param.information_file, 'permuted link invalid. Continuing..', 'moved forward:', index_moved_forward, 'shifted:', index_shifted
- return None, None, None, None
-
-
- #print i1,i2 #'OBSLIST_', observations[(c1,c2)]
- #observations = map(lambda x: (contigs_to_indexes[x[0][0]], contigs_to_indexes[x[1][0]]) = observations[x], observations)
-
- #print 'MP LINK RATIO:{0}, tot_links:{1}'.format(mp_links/float(tot_links), tot_links)
- #print index_observations
- #print ctg_lengths_index_ordered
- #print index_observations
-
- ## 2 Get optimal LP solution for given path order
- result_path = order_contigs.main(ctg_lengths_index_ordered, index_observations, param)
- if not result_path:
- print 'We should never end up here!'
- return None,None,None,None
-
- return result_path, contigs_to_indexes, indexes_to_contigs, index_observations
-
-
-def path_permutations_iterator(path, i, original_path):
- """
- Iterator function to return all "valid" permutations of contigs given our
- assumptions of links. This is a very limited set of permutations compared to the m!
- if m contigs
- blowup of a general permutation set. For small instances (m < 5), this will return 2^m
- permutations. If m is larger, we return 2^5 + 2^5 + ... +2^(rest < 5) permutations where the sum
- contians m/5 +1 terms. This is a huristic but well motivated by the fact that far away contigs in initial
- solution is unlikely to be permuted so that they switch order with each other. (This depends on the isize of course)
-
- Another heuristic could be to instead of chosing 5, we scale down 2^m for large m by
- giving back all permutations of sets of contigs that have sum of lenghts larger than, say, mu+3sigma. This
- is another way of separating and scaling down the solution space by using the fact that far away contigs
- in initial solution is unlikely to be permuted so that they switch order with each other.
-
- In original_path : switch is always performed on contig i with contig i-1. Since each
- contig except start and en here has 2 nodes in the path object, we will always permute
- items [i,i+1] with items [i-2,i-1] in original path, where i =3, 5, 7,..., len(path) - 3.
- Object on index len(path)-1 in the list (last object) is the right border contig.
- """
- #Path needs to be a deepcopy of original_path !!!!
- if 3<= i <= len(original_path)-3:
- # no permutation
- #yield path
- #print '1lol',i,path
- for p in path_permutations_iterator(copy.deepcopy(path), i+2, original_path):
- yield p #path_permutations_iterator(path, i+2, original_path)
-
- ### permuting ###
- #contigs to permute
- c1_x, c1_y, c2_x, c2_y = original_path[i-2],original_path[i-1],original_path[i],original_path[i+1]
- # current indexes of them in path
- i_c1_x, i_c1_y, i_c2_x, i_c2_y = path.index(c1_x), path.index(c1_y), path.index(c2_x), path.index(c2_y)
-
- # permutation is that i_c2_x --> i_c1_x , i_c2_y --> i_c1_y and all contigs after that
- # is shited 2 indicies up
- path.insert(i_c1_x, path.pop(i_c2_x))
- path.insert(i_c1_x+1, path.pop(i_c2_y))
-
- # path.insert(pos_of_ctg_after, (ctg_to_move,'L') )
- # path.insert(pos_of_ctg_after, (ctg_to_move,'R') )
- # path.insert(pos_of_ctg_after, (ctg_to_move,'R') )
- # path.insert(pos_of_ctg_after, (ctg_to_move,'L') )
-
-
- # path[i_c1_x],path[i_c1_y],path[i_c2_x],path[i_c2_y] = path[i_c2_x],path[i_c2_y],path[i_c1_x],path[i_c1_y]
- #yield path
- #print '2lol',i,path
- for p in path_permutations_iterator(copy.deepcopy(path), i+2, original_path):
- yield p #path_permutations_iterator(path, i+2, original_path)
- else:
- yield path
-
-
-
-def path_permutations_with_overlap_constraints(original_path, constraint_dict):
- """
- Iterator function to return all "valid" permutations of contigs given overlap constraints.
- This is a very limited set of permutations compared to the m!
- if m contigs.
- """
- # # Adjacancies of valid permutations according to our model
- # path = copy.deepcopy(original_path)
- # valid_permutations = set()
- # for i in range(3, len(path) - 1, 2):
- # # switch positions of two contigs
- # ctg_end = original_path[i]
- # contig_end = original_path[i-2]
- # #
-
- # order original path with the constraint pairs
- path = copy.deepcopy(original_path)
- print "before constraints", path
-
- long_end = path[0]
- long_beginning = path[-1]
-
- for beginning in constraint_dict:
- c2_x = beginning
- c1_y = constraint_dict[beginning][0]
-
- if c2_x == long_beginning and c1_y == long_end:
- continue
-
- #print c1_y,c2_x
- i_c2_x = path.index(c2_x)
-
- i_c1_y = path.index(c1_y)
-
- #print 'HHEHER', i_c1_y, i_c2_x
-
-
- if c2_x == long_beginning:
- # print '1', path
- i_c1_x = i_c1_y - 1
- c1_x = path[i_c1_x]
- path.insert(-1, c1_x)
- path.insert(-1, c1_y)
- path.pop(i_c1_y)
- path.pop(i_c1_x)
- # print '5', path
- continue
-
-
-
- if c1_y == long_end:
- # print '1', path
- i_c2_y = i_c2_x+1
- c2_y = path[i_c2_y]
- path.insert(1, c2_y)
- path.insert(1, c2_x)
- path.pop(i_c2_y+2)
- path.pop(i_c2_x+2)
- # print '5', path
- continue
-
- i_c1_x = i_c1_y - 1
- c1_x = path[i_c1_x]
- i_c2_y = i_c2_x+1
- c2_y = path[i_c2_y]
-
- if i_c1_y < i_c2_x:
- # print '1', path
- path.insert(i_c2_x, c1_y)
- # print '2', path
- path.pop(i_c1_y)
- # print '3', path
- path.insert(i_c2_x-1, c1_x)
- # print '4', path
- path.pop(i_c1_x)
- # print '5', path
-
- elif i_c2_x < i_c1_y:
- # print '1lolz', path
- path.insert(i_c1_y, path.pop(i_c2_x))
- path.insert(i_c1_y, path.pop(i_c2_x))
- # print '5', path
-
- print "after constraints", path
-
- return path
-
-
-
-
-rev_nuc = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'a':'t', 'c':'g', 'g':'c', 't':'a', 'N':'N', 'X':'X', 'n':'n', 'Y':'R', 'R':'Y', 'K':'M', 'M':'K', 'S':'S', 'W':'W', 'B':'V', 'V':'B', 'H':'D', 'D':'H', 'y':'r', 'r':'y', 'k':'m', 'm':'k', 's':'s', 'w':'w', 'b':'v', 'v':'b', 'h':'d', 'd':'h'}
-
-def rev_comp(string, rev_nuc):
- #rev_nuc={'A':'T','C':'G','G':'C','T':'A','N':'N','X':'X'}
- rev_comp = ''.join([rev_nuc[nucl] for nucl in reversed(string)])
- return(rev_comp)
-
-def check_kmer_overlap(end1,end2):
- i = len(end1)
- while i > 0:
- if end1[-i:] == end2[:i]:
- return i
- i -= 1
- return i
-
-def kmer_overlaps(path, Scaffolds, small_scaffolds, Contigs, small_contigs):
-
- # get sequences of contigs
- seq_dict = {} # "ctg_sequence" : "scaf_index"
- label_dict_beginnings = {}
- label_dict_ends = {}
- # print path
- for label in path:
- # get each end of 200bp
-
- # scaffold is forward oriented and beginning
- if (label[1] == 'L' and path.index(label) % 2 == 1):
- #print Scaffolds[label[0]].contigs, Scaffolds[label[0]].contigs[0].direction
- ctg = Scaffolds[label[0]].contigs[0]
- #print ctg.sequence
- if ctg.direction:
- ctg_seq = ctg.sequence[:200]
- else:
- ctg_seq = rev_comp(ctg.sequence[-200:], rev_nuc)
- label_dict_beginnings[label] = ctg_seq
-
- # scaffold is forward oriented and end
- elif (label[1] == 'R' and path.index(label) % 2 == 0):
- ctg = Scaffolds[label[0]].contigs[-1]
- #print ctg.sequence
- if ctg.direction:
- ctg_seq = ctg.sequence[-200:]
- else:
- ctg_seq = rev_comp(ctg.sequence[:200], rev_nuc)
- label_dict_ends[label] = ctg_seq
-
- # scaffold is reverse oriented and beginning
- elif (label[1] == 'R' and path.index(label) % 2 == 1):
- ctg = Scaffolds[label[0]].contigs[-1]
- if ctg.direction:
- ctg_seq = rev_comp(ctg.sequence[-200:], rev_nuc)
- else:
- ctg_seq = ctg.sequence[:200]
- label_dict_beginnings[label] = ctg_seq
-
- # scaffold is reverse oriented and end
- elif (label[1] == 'L' and path.index(label) % 2 == 0):
- ctg = Scaffolds[label[0]].contigs[0]
- if ctg.direction:
- # print "LLLOOOOL"
- ctg_seq = rev_comp(ctg.sequence[-200:], rev_nuc) #[::-1]
- else:
- ctg_seq = ctg.sequence[-200:]
- label_dict_ends[label] = ctg_seq
-
- else:
- print 'BUG!'
-
- #label_dict[label] = ctg_seq
-
- already_added = set()
- constraint_pairs = {}
- constraint_dict = {}
-
- for label1 in label_dict_ends:
- for label2 in label_dict_beginnings:
- if label1[0] != label2[0]:
- overlap = check_kmer_overlap(label_dict_ends[label1], label_dict_beginnings[label2])
- if overlap > 20:
- print overlap
- # print overlap, label1, label2
- # print label_dict[label1], label_dict[label2]
- # print
- if label1 not in already_added and label2 not in already_added:
- #print 'YEAH', already_added
- constraint_pairs[label1] = (label2, overlap)
- constraint_dict[label2] = (label1, overlap)
- already_added.add(label1)
- already_added.add(label2)
-
- elif label1 in already_added and label2 not in already_added:
- old_label2 = constraint_pairs[label1][0]
- if overlap > constraint_pairs[label1][1]:
- del constraint_pairs[label1]
- del constraint_dict[old_label2]
- constraint_pairs[label1] = (label2, overlap)
- constraint_dict[label2] = (label1, overlap)
- already_added.add(label1)
- already_added.add(label2)
- already_added.remove(old_label2)
-
- elif label1 not in already_added and label2 in already_added:
- old_label1 = constraint_dict[label2][0]
- if overlap > constraint_dict[label2][1]:
- del constraint_dict[label2]
- del constraint_pairs[old_label1]
- constraint_dict[label2] = (label1, overlap)
- constraint_pairs[label1] = (label2, overlap)
- already_added.add(label1)
- already_added.add(label2)
- already_added.remove(old_label1)
-
- elif label1 in already_added and label2 in already_added:
- old_label1 = constraint_dict[label2][0]
- old_label2 = constraint_pairs[label1][0]
- if overlap > constraint_dict[label2][1] and overlap > constraint_pairs[label1][1]:
- del constraint_dict[label2]
- del constraint_pairs[old_label1]
- del constraint_pairs[label1]
- del constraint_dict[old_label2]
- constraint_dict[label2] = (label1, overlap)
- constraint_pairs[label1] = (label2, overlap)
- already_added.add(label1)
- already_added.add(label2)
- already_added.remove(old_label1)
- already_added.remove(old_label2)
-
- # else:
- # constraint_pairs[label1] = (label2, overlap)
-
-
- #print already_added
-
- #''.join(map(lambda ctg: ctg.sequence, Scaffolds[label[0]].contigs[0]))
-
- # find longest overlaps
-
- # generate and return constraints on permutations
-
- return constraint_dict
-
-
-def permute_path_segment(path, ctg_to_move, ctg_after, valid_connections):
- #print 'path before permute', path
- segment_upper_index = max(path.index((ctg_to_move, 'L')), path.index((ctg_to_move, 'R')))
- segment_min_index = max(path.index((ctg_after, 'L')), path.index((ctg_after, 'R'))) + 1
- segment_lower_index = segment_min_index
- for index in range(segment_upper_index, segment_min_index, -1):
- if path[index][0] == path[index-1][0] or (path[index][0], path[index-1][0]) in valid_connections or (path[index-1][0], path[index][0]) in valid_connections:
- continue
- else:
- segment_lower_index = index
-
- segment_to_move = path[segment_lower_index: segment_upper_index + 1]
- #print "segment to move", segment_to_move
- path[segment_lower_index: segment_upper_index + 1] = []
- permuted_path = path[0:segment_min_index-2] + segment_to_move + path[segment_min_index-2:]
- #print "path after permute", permuted_path
- return permuted_path
-
-
-def calculate_min_objective(path, Scaffolds, small_scaffolds, observations, param, valid_permutations, valid_connections):
- current_min_path = copy.deepcopy(path)
- current_min_path_instance, current_min_contigs_to_indexes, current_min_indexes_to_contigs, current_min_index_observations = calculate_path_LP(current_min_path, Scaffolds, small_scaffolds, observations, param)
- ctgs_perm_chosen = None
- #print 'WORK IS DONE'
-
- for edge_end1, edge_end2 in valid_permutations:
- # switch positions of two contigs
- #print "To permute:", edge_end1, edge_end2
- current_path = copy.deepcopy(path)
- ctg_to_move = edge_end1[0]
- ctg_after = edge_end2[0]
- current_path = permute_path_segment(current_path, ctg_to_move, ctg_after, valid_connections)
-
- #print 'Current current_path:',current_path
- ## 1 Get a mapping from contigs to indexes (index for contig order in the current current_min_path)
- current_path_instance, current_contigs_to_indexes, current_indexes_to_contigs, current_index_observations = calculate_path_LP(current_path, Scaffolds, small_scaffolds, observations, param, moved_forward=ctg_to_move, shifted=ctg_after)
- if not current_path_instance:
- continue
- ## 3 Check of current current_min_path is better than previous
- #print 'Current objective: {0}, best objective: {1}'.format(current_path_instance.objective, current_min_path_instance.objective)
- # if -1 < current_path_instance.objective - current_min_path_instance.objective < 1:
- # print 'Very close:', current_path_instance.objective, current_min_path_instance.objective
- # print current_path_instance.objective < current_min_path_instance.objective
- #print 'obj:', current_path_instance.objective,current_min_path_instance.objective
- if current_path_instance.objective < current_min_path_instance.objective - 1:
- current_min_path = copy.deepcopy(current_path)
- current_min_path_instance = copy.deepcopy(current_path_instance)
- current_min_contigs_to_indexes = current_contigs_to_indexes
- current_min_indexes_to_contigs = current_indexes_to_contigs
- current_min_index_observations = current_index_observations
- ctgs_perm_chosen = (edge_end1, edge_end2)
- #print "IN FCN:", ctgs_perm_chosen, current_min_path_instance.objective
- return current_min_path, current_min_path_instance, current_min_contigs_to_indexes, current_min_indexes_to_contigs, current_min_index_observations, ctgs_perm_chosen
-
-
-
-def estimate_path_gaps(Contigs, small_contigs, path,Scaffolds,small_scaffolds, G_prime, param):
- #print "New path!"
- ## ACCURATE GAP EST HERE
-
- #print G_prime.subgraph(path).edges(data=True)
- sub_graph = G_prime.subgraph(path)
-
-
- #print G_prime.subgraph(path).edges(data=True)
- sub_graph_reduced = filter(lambda x: sub_graph[x[0]][x[1]]['nr_links'] != None and x[0][0] in sub_graph[x[0]][x[1]] , sub_graph.edges())
-
- observations = dict(map(lambda x: (x, [i+j for i,j in zip(sub_graph[x[0]][x[1]][x[0][0]], sub_graph[x[0]][x[1]][x[1][0]] )]), sub_graph_reduced))
- sub_graph_small_to_large_ctgs = filter(lambda x: sub_graph[x[0]][x[1]]['nr_links'] != None and x[0][0] not in sub_graph[x[0]][x[1]] , sub_graph.edges())
- for c1,c2 in sub_graph_small_to_large_ctgs:
- #observations[(c1,c2)] = (sub_graph[c1][c2]['obs']/ sub_graph[c1][c2]['nr_links'], sub_graph[c1][c2]['nr_links']) #[sub_graph[c1][c2]['obs']/ sub_graph[c1][c2]['nr_links']]*sub_graph[c1][c2]['nr_links']
- n = sub_graph[c1][c2]['nr_links']
- mean_obs = sub_graph[c1][c2]['obs'] / n
- if n > 1:
- std_dev_obs = ((sub_graph[c1][c2]['obs_sq'] - n * mean_obs ** 2) / (n - 1)) ** 0.5
- else:
- std_dev_obs = 0
- obs_list = sub_graph[c1][c2]['observations']
- observations[(c1, c2)] = (mean_obs, n, std_dev_obs, obs_list)
-
- # for c1,c2 in observations:
- # if (other_end(c2),other_end(c1)) in observations:
- # print observations
- # print param.contamination_ratio
-
-
-
- #########################
- ##########################
- ## Now we have all info that we need to send to module for calculating optimal path
-
-
- # only one contig, nothing to permute
- if len(path) <= 4 or not param.contamination_ratio or param.NO_ILP:
-
- # constraint_pairs = kmer_overlaps(path, Scaffolds, small_scaffolds, Contigs, small_contigs)
- # print 'small', constraint_pairs
-
- final_path_instance, final_contigs_to_indexes, final_indexes_to_contigs, final_index_observations = calculate_path_LP(path,Scaffolds,small_scaffolds,observations,param)
- final_path = path
- #print final_path
-
- ## algm here
- else:
-
-
- # new algorithm
- # final_path_instance, final_contigs_to_indexes, final_indexes_to_contigs, final_index_observations = calculate_path_LP(path,Scaffolds,small_scaffolds,observations,param)
- # final_path = copy.deepcopy(path)
- # original_path = copy.deepcopy(path)
-
- # for p in path_permutations_iterator(path, 3, original_path):
- # print p
- # ## 1 Get a mapping from contigs to indexes (index for contig order in the current path)
- # current_path_instance, current_contigs_to_indexes, current_indexes_to_contigs, current_index_observations = calculate_path_LP(p,Scaffolds,small_scaffolds,observations,param)
- # if not current_path_instance:
- # continue
- # ## 3 Check of current path is better than previous
- # if current_path_instance.objective < final_path_instance.objective:
- # final_path = copy.deepcopy(p)
- # final_path_instance = copy.deepcopy(current_path_instance)
- # final_contigs_to_indexes = current_contigs_to_indexes
- # final_indexes_to_contigs = current_indexes_to_contigs
- # final_index_observations = current_index_observations
- ############################
-
-
-
- ## overlap idea ##
-
- # original_path = copy.deepcopy(path)
- # constraint_dict = kmer_overlaps(path, Scaffolds, small_scaffolds, Contigs, small_contigs)
- # print 'big', constraint_dict
- # original_path_with_constraints = path_permutations_with_overlap_constraints(original_path, constraint_dict)
-
- # final_path_instance, final_contigs_to_indexes, final_indexes_to_contigs, final_index_observations = calculate_path_LP(original_path_with_constraints, Scaffolds, small_scaffolds, observations,param)
- # final_path = copy.deepcopy(original_path_with_constraints)
-
- # end_constraints = map(lambda x: x[0], constraint_dict.values())
- # # inital valid permutations
- # for i in range(3, len(path) - 1, 2):
- # # switch positions of two contigs
- # contig_beginning = original_path[i]
- # contig_end = original_path[i-2]
- # if contig_beginning in constraint_dict or contig_end in end_constraints:
- # continue
- # else:
- # # switch positions of two contigs
- # current_path = copy.deepcopy(final_path)
- # print current_path
- # ctg_to_move = original_path[i][0]
- # contig_after = original_path[i-2][0]
- # current_path = permute_path(current_path, ctg_to_move, contig_after)
-
- # #print 'Current path:',current_path
- # ## 1 Get a mapping from contigs to indexes (index for contig order in the current path)
- # current_path_instance, current_contigs_to_indexes, current_indexes_to_contigs, current_index_observations = calculate_path_LP(current_path,Scaffolds,small_scaffolds,observations,param)
- # if not current_path_instance:
- # continue
- # ## 3 Check of current path is better than previous
- # #print 'Current objective: {0}, best objective: {1}'.format(current_path_instance.objective, final_path_instance.objective)
-
- # if current_path_instance.objective < final_path_instance.objective:
- # final_path = copy.deepcopy(current_path)
- # final_path_instance = copy.deepcopy(current_path_instance)
- # final_contigs_to_indexes = current_contigs_to_indexes
- # final_indexes_to_contigs = current_indexes_to_contigs
- # final_index_observations = current_index_observations
-
-
-
- #########################
-
-
-
- if param.FASTER_ILP:
-
- #### ORIGINAL ILP ##############
-
- final_path_instance, final_contigs_to_indexes, final_indexes_to_contigs, final_index_observations = calculate_path_LP(path,Scaffolds,small_scaffolds,observations,param)
- final_path = copy.deepcopy(path)
- original_path = copy.deepcopy(path)
- #print 'WORK IS DONE'
-
- for i in range(3, len(path) - 1, 2):
- # switch positions of two contigs
- current_path = copy.deepcopy(final_path)
- ctg_to_move = original_path[i][0]
- contig_after = original_path[i-2][0]
- current_path = permute_path(current_path, ctg_to_move, contig_after)
-
- #print 'Current path:',current_path
- ## 1 Get a mapping from contigs to indexes (index for contig order in the current path)
- current_path_instance, current_contigs_to_indexes, current_indexes_to_contigs, current_index_observations = calculate_path_LP(current_path, Scaffolds, small_scaffolds, observations, param, moved_forward=ctg_to_move, shifted=contig_after)
- if not current_path_instance:
- continue
- ## 3 Check of current path is better than previous
- #print 'Current objective: {0}, best objective: {1}'.format(current_path_instance.objective, final_path_instance.objective)
- if -1 < current_path_instance.objective - final_path_instance.objective < 1:
- print 'Very close:', current_path_instance.objective, final_path_instance.objective
- print current_path_instance.objective < final_path_instance.objective
-
- if current_path_instance.objective < final_path_instance.objective - 1:
- final_path = copy.deepcopy(current_path)
- final_path_instance = copy.deepcopy(current_path_instance)
- final_contigs_to_indexes = current_contigs_to_indexes
- final_indexes_to_contigs = current_indexes_to_contigs
- final_index_observations = current_index_observations
-
- #########################################################################
-
-
- ### O(n*(n-1)/2) solution idea ######
-
- else:
- max_nr_rounds = len(range(3, len(path) - 1, 2))
- current_min_path = copy.deepcopy(path)
-
- # calculate initial round with all edges
- valid_permutations = set([(current_min_path[i], current_min_path[i-2]) for i in range(3, len(path) - 1, 2)])
- #print "PERM set:", valid_permutations
-
- # store what are valid adjacent contigs, we need it as info when we permute contigs in a path
- valid_connections = set([(current_min_path[i][0], current_min_path[i-2][0]) for i in range(3, len(path) - 1, 2)])
-
- final_path, final_path_instance, final_contigs_to_indexes, final_indexes_to_contigs, final_index_observations, ctgs_perm_chosen = calculate_min_objective(current_min_path, Scaffolds, small_scaffolds, observations, param, valid_permutations, valid_connections)
-
- # In initial step, at least one solution was better than original path
- if ctgs_perm_chosen:
- valid_permutations.remove(ctgs_perm_chosen)
- #print "PERM set:", valid_permutations
- i = 1
- while i < max_nr_rounds:
- #print 'WE are here!!!!! round:', i, max_nr_rounds
- min_path, min_solution_path_instance, min_solution_contigs_to_indexes, min_solution_indexes_to_contigs, min_solution_index_observations, ctgs_perm_chosen = calculate_min_objective(final_path,Scaffolds,small_scaffolds,observations,param, valid_permutations, valid_connections)
- #print "IN WHILE:", ctgs_perm_chosen
- if ctgs_perm_chosen:
- valid_permutations.remove(ctgs_perm_chosen)
- else:
- break
- #print "PERM set LOLLL:", valid_permutations
- # allow smal approximation error of LP solver, hence at least -1 lower obj of new instance is accepted
- if min_solution_path_instance.objective < final_path_instance.objective - 1:
- final_path = copy.deepcopy(min_path)
- final_path_instance = copy.deepcopy(min_solution_path_instance)
- final_contigs_to_indexes = min_solution_contigs_to_indexes
- final_indexes_to_contigs = min_solution_indexes_to_contigs
- final_index_observations = min_solution_index_observations
- else:
- break
- i += 1
-
-
- ######################################
-
-
-
-
-
- ## 5 Calculate some stats on the path that we have chosen
-
- param.path_gaps_estimated += len(final_path_instance.gaps)
- path_dict_index = final_path_instance.make_path_dict_for_besst()
- #print 'FINAL:', final_path
- #print 'OBJECTIVE: {0}'.format(final_path_instance.objective)
-
- # for ctg in final_path:
- # if ctg[0] in Scaffolds:
- # for c in Scaffolds[ctg[0]].contigs:
- # print 'ctg name, scaffold{0}: {1}'.format(ctg[0],c.name)
- # else:
- # print 'small ctg name:', small_scaffolds[ctg[0]].contigs[0].name
-
-
- #print final_path_instance
- #print path_dict_index
- path_dict = map(lambda x: (final_indexes_to_contigs[x[0].index],final_indexes_to_contigs[x[1].index], path_dict_index[x]), path_dict_index)
- #print path_dict
- # for ctg in final_path_instance.ctgs:
- # contig = indexes_to_contigs[ctg.index]
- # ctg.length
- # ctg.position
-
- G_ = nx.Graph()
- final_path.insert(0, (final_path[0][0], 'R')) if final_path[0][1] == 'L' else final_path.insert(0, (final_path[0][0], 'L'))
- final_path.insert(len(final_path), (final_path[-1][0], 'R')) if final_path[-1][1] == 'L' else final_path.insert(len(final_path), (final_path[-1][0], 'L'))
- G_.add_edges_from(zip(final_path[::1], final_path[1::]))
-
- for c1,c2,gap in path_dict:
- if (c2,'L') in G_[(c1,'L')]:
- G_[(c1,'L')][(c2,'L')]['avg_gap'] = gap
- elif (c2,'R') in G_[(c1,'L')]:
- G_[(c1,'L')][(c2,'R')]['avg_gap'] = gap
- elif (c2,'L') in G_[(c1,'R')]:
- G_[(c1,'R')][(c2,'L')]['avg_gap'] = gap
- elif (c2,'R') in G_[(c1,'R')]:
- G_[(c1,'R')][(c2,'R')]['avg_gap'] = gap
- else:
- print 'Could not find edge!'
- sys.exit()
- #print G_.edges(data=True)
-
- return(G_, final_path)
-
-
-def PROBetweenScaf(G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, param, dValuesTable, Information):
- start_scaf_index = param.scaffold_indexer
- G = nx.Graph()
- for node in G_prime:
- if node[0] in Scaffolds: # meets the length criteria
- G.add_node(node)
-
- # Filtering and heuristic here to reduce computation if needed O(n^2) in contigs on pathfinder
-
- #remove all solated contigs
- for node in G.nodes():
- if node in G:
- nbr = G_prime.neighbors(node)[0]
- if len(G_prime.neighbors(node)) == 1 and len(G_prime.neighbors(nbr)) == 1:
- G.remove_nodes_from([node, nbr])
-
-
- if len(G.nodes()) / 2.0 > 10000:
- # Too few short contigs compared to long (ratio set to 0.1) or lib ins size + 2*std_dev - 2*read_len < 200 ) and too many large contigs (> 10 000) do not enter path extension algm since to low payoff:
-
- if len(small_scaffolds) / float(len(Scaffolds)) < 0.1:
- print >> Information, "Did not enter path seartching algorithm between scaffolds due to too small fraction of small scaffolds, fraction were: ", len(small_scaffolds) / float(len(Scaffolds))
- return(start_scaf_index)
-
- ########### Find paths between scaffolds here ###############
-
- # Multi Processing (if available), check nr of available cores
- num_cores = multiprocessing.cpu_count()
- #TODO: If we get too many paths back and run into memory issues we could change so that only paths with score over 0 are stored in ELS module
- if param.multiprocess and num_cores > 1:
- import workerprocess
- import heapq
- print >> Information, 'Entering ELS.BetweenScaffolds parallelized with ', num_cores, ' cores.'
- start = time.time()
- # load up work queue
- work_queue = multiprocessing.Queue()
- end = set()
- for node in G:
- end.add(node)
- nodes = G.nodes()
- nr_jobs = len(nodes)
- chunk = nr_jobs / (num_cores)
- counter = 0
- nr_processes = 0
- # partition equally many nodes in G to each core
- while counter < nr_jobs:
- work_queue.put((set(nodes[counter:counter + chunk]), G_prime, end, param))
- nr_processes += 1
- print >> Information, 'node nr', counter, 'to', counter + chunk - 1, 'added'
- #print work_queue.get()
- counter += chunk
-
- # create a queue to pass to workers to store the results
- result_queue = multiprocessing.Queue()
-
- # spawn workers
- while not work_queue.empty():
- worker = workerprocess.Worker(work_queue.get(), result_queue)
- worker.start()
-
- # collect the results off the queue
- results = []
- for i in range(nr_processes):
- res = result_queue.get()
- results.append(res)
-
- def wrapper(func, args):
- return(func(*args))
- all_paths_sorted_wrt_score_itr = wrapper(heapq.merge, results) #tot_result
- all_paths_sorted_wrt_score = [i for i in all_paths_sorted_wrt_score_itr]
- elapsed = time.time() - start
- print >> Information, "Elapsed time multiprocessing: ", elapsed
-
- else:
- start = time.time()
- end = set()
- for node in G:
- end.add(node)
- iter_nodes = end.copy()
- print >> Information, 'Entering ELS.BetweenScaffolds single core'
- all_paths_sorted_wrt_score = ELS.BetweenScaffolds(G_prime, end, iter_nodes, param)
- elapsed = time.time() - start
- print >> Information, "Elapsed time single core pathfinder: ", elapsed
- print "Elapsed time single core pathfinder: ", elapsed
-
- ################################################################
-
- nr_paths = len(all_paths_sorted_wrt_score)
- start_end_node_update_storage = {}
- print >> Information, '{0} paths detected are with score greater or equal to {1} '.format(nr_paths, param.score_cutoff)
- for sublist in reversed(all_paths_sorted_wrt_score):
- path = sublist[2]
- bad_links = sublist[1]
- score = sublist[0]
- path_len = sublist[3]
- if nr_paths <= 100000:
- print >> Information, 'Path: path length: {0}, nr bad links: {1}, score: {2} '.format((path_len - 2) / 2.0, bad_links, score)
-
- ## Need something here that keeps track on which contigs that are added to Scaffolds so that a
- ## contig is only present once in each path
-
- #print start_end_node_update_storage
- # Either a small contig/scaffold has been included in a path earlier and thus has moved it's object to Scaffolds (and changed index)
- small_scaf_is_already_in = 0
- for scaf_ in path[1:-1]:
- if scaf_[0] not in small_scaffolds:
- small_scaf_is_already_in = 1
- #print 'At least one of the contigs is already in another scaffold'
- break
- if small_scaf_is_already_in:
- continue
-
- # A very special corner case (circular paths)
- if path[0][0] not in Scaffolds and path[-1][0] not in Scaffolds:
- try:
- strt = start_end_node_update_storage[path[0]][0]
- nd = start_end_node_update_storage[path[-1]][0]
- if strt[0] == nd[0]:
- print >> Information, 'Rare case (circular paths) detected and treated. '
- continue
- except KeyError:
- pass
-
- # Or a large scaffold/contig has changed scaffold index due to one of it's sides is present in another path (we still want to allow for paths from the other side)
- case1 = 0
- case2 = 0
- if path[0][0] not in Scaffolds:
- if path[0] in start_end_node_update_storage:
- case1 = 1
- else:
- print >> Information, 'Beginning is already in path'
- continue
-
- if path[-1][0] not in Scaffolds:
- if path[-1] in start_end_node_update_storage:
- case2 = 1
- else:
- print >> Information, 'End is already in path'
- continue
-
-
- original_start_node = path[0]
-
- if path[0][0] not in Scaffolds:
- #large scaffold has changed index before. This suggested path is however from it's other side
- node_to_remove1 = path[0]
- path[0] = start_end_node_update_storage[node_to_remove1][0]
- #update the node on the other end of the end scaffold to point at the newest index
- node_to_refresh1 = start_end_node_update_storage[node_to_remove1][1]
- #print 'Enter 1'
- try:
- node_ptr = start_end_node_update_storage[ path[-1] ][1]
- #print '1.1', node_ptr,start_end_node_update_storage[ path[-1] ]
- except KeyError:
- other_side = 'L' if path[-1][1] == 'R' else 'R'
- node_ptr = (path[-1][0], other_side)
- #print '1.2', node_ptr, path[-1]
- start_end_node_update_storage[node_to_refresh1] = [(param.scaffold_indexer + 1, 'L'), node_ptr ]
- #path pointer can be accesed only once needs to be destroyed after
- del start_end_node_update_storage[node_to_remove1]
-
-
- if path[-1][0] not in Scaffolds:
- #large scaffold has changed index before. This suggested path is however from it's other side
- #print 'case2.2'
- node_to_remove2 = path[-1]
- path[-1] = start_end_node_update_storage[node_to_remove2][0]
- #update the node on the other end of the end scaffold to point at the newest index
- node_to_refresh2 = start_end_node_update_storage[node_to_remove2][1]
- #print 'Enter 2'
- try:
- node_ptr = start_end_node_update_storage[ original_start_node ][1]
- #print '2.1', node_ptr, start_end_node_update_storage[ original_start_node ]
- except KeyError:
- other_side = 'L' if original_start_node[1] == 'R' else 'R'
- node_ptr = (original_start_node[0], other_side)
- #print '2.2', node_ptr,original_start_node
- start_end_node_update_storage[node_to_refresh2] = [(param.scaffold_indexer + 1, 'R'), node_ptr ]
- #path pointer can be accesed only once needs to be destroyed after
- del start_end_node_update_storage[node_to_remove2]
-
-
- # Here we update the contigs that lies in small_contigs to Contigs. We need to do this here because
- # we update the scaffold index below
-
- # move all contig and scaffold objects from "small" structure to large structure to fit with UpdateInfo structure
-
- small_scafs = map(lambda i: path[i], filter(lambda i: i % 2 == 1, range(len(path) - 1)))
- for item in small_scafs:
- scaf_obj = small_scaffolds[item[0]]
- Scaffolds[item[0]] = scaf_obj
- cont_objects = scaf_obj.contigs
- for obj_ in cont_objects:
- ctg_name = obj_.name
- Contigs[ctg_name] = obj_
- del small_contigs[ctg_name]
- del small_scaffolds[item[0]]
- ## Here we do the "joining of two scaffolds with the new path if no contig/scaffold is present
- ## in another path, we need to update "Scaffolds" structure here along as we go in order for
- ## the above dublette checking function to work
-
-
- G_, path = estimate_path_gaps(Contigs, small_contigs, path,Scaffolds,small_scaffolds, G_prime,param)
-
-
- # #make the path a small linear graph
- # G_ = nx.Graph()
- # path.insert(0, (path[0][0], 'R')) if path[0][1] == 'L' else path.insert(0, (path[0][0], 'L'))
- # path.insert(len(path), (path[-1][0], 'R')) if path[-1][1] == 'L' else path.insert(len(path), (path[-1][0], 'L'))
- # G_.add_edges_from(zip(path[::1], path[1::]))
-
- start_end_node_update_storage[path[0]] = 0
- start_end_node_update_storage[path[-1]] = 0
-
-
- start = path[0]
- end = path[-1]
- prev_node = ('', '')
- pos = 0
- scaffold_length = 0
- contig_list = []
- param.scaffold_indexer += 1
-
- values = UpdateInfo(G_, Contigs, small_contigs, Scaffolds, small_scaffolds, start, prev_node, pos, contig_list, scaffold_length, dValuesTable, param)
- #print values
- while len(values) !=2:
- values = UpdateInfo(G_,*values)
-
- (contig_list, scaffold_length) = values[0],values[1]
- S = Scaffold.scaffold(param.scaffold_indexer, contig_list, scaffold_length) #Create the new scaffold object
-
- if nr_paths <= 100000:
- print >> Information, 'Path taken! path length: {0}, nr bad links: {1}, score: {2} '.format((path_len - 2) / 2.0, bad_links, score)
-
- Scaffolds[S.name] = S #include in scaffold library
- #add the new scaffold object to G_prime
-
- G_prime.add_node((S.name, 'L')) #start node
- G_prime.add_node((S.name, 'R')) # end node
- G_prime.add_edge((S.name, 'L'), (S.name, 'R'), nr_links=None)
- for nbr in G_prime.neighbors(start):
- nr_links_ = G_prime[start][nbr]['nr_links']
- if nr_links_:
- obs_ = G_prime[start][nbr]['obs']
- observations_ = G_prime[start][nbr]['observations']
- #G_prime.add_edge((S.name, 'L'), nbr, nr_links=nr_links_, obs=obs_)
- obs_sq_ = G_prime[start][nbr]['obs_sq']
- G_prime.add_edge((S.name, 'L'), nbr, nr_links=nr_links_, obs=obs_, obs_sq=obs_sq_, observations=observations_)
-
- for nbr in G_prime.neighbors(end):
- nr_links_ = G_prime[end][nbr]['nr_links']
- if nr_links_:
- obs_ = G_prime[end][nbr]['obs']
- observations_ = G_prime[end][nbr]['observations']
- # G_prime.add_edge((S.name, 'R'), nbr, nr_links=nr_links_, obs=obs_)
- obs_sq_ = G_prime[end][nbr]['obs_sq']
- G_prime.add_edge((S.name, 'R'), nbr, nr_links=nr_links_, obs=obs_, obs_sq=obs_sq_, observations=observations_)
-
- #remove the old scaffold objects from G_prime
- G_prime.remove_nodes_from(path)
-
- #updated beginning
- if case1 and not case2:
- start_end_node_update_storage[node_to_refresh1] = [(S.name, 'L'), path[-1] ]
- start_end_node_update_storage[path[-1]] = [(S.name, 'R'), node_to_refresh1 ]
- elif case2 and not case1:
- start_end_node_update_storage[path[0]] = [(S.name, 'L'), node_to_refresh2 ]
- start_end_node_update_storage[node_to_refresh2] = [(S.name, 'R'), path[0] ]
- elif case1 and case2:
- start_end_node_update_storage[node_to_refresh1] = [(S.name, 'L'), node_to_refresh2 ]
- start_end_node_update_storage[node_to_refresh2] = [(S.name, 'R'), node_to_refresh1 ]
- else:
- start_end_node_update_storage[path[0]] = [(S.name, 'L'), path[-1] ]
- start_end_node_update_storage[path[-1]] = [(S.name, 'R'), path[0] ]
-
- return(start_scaf_index)
-
-def GiveLinkConnection(Contigs, contig_objects1, contig_objects2, side1, side2, nr_links):
- if side1 == 'R' and side2 == 'L':
- max_pos = 0
- for contig in contig_objects1:
- if contig.position >= max_pos:
- linking_contig1 = contig
- max_pos = contig.position
- min_pos = sys.maxint
- for contig in contig_objects2:
- if contig.position <= min_pos:
- linking_contig2 = contig
- min_pos = contig.position
-
- linking_contig1.links[linking_contig2.name] = nr_links
- linking_contig2.links[linking_contig1.name] = nr_links
-
-
- elif side1 == 'L' and side2 == 'R':
- max_pos = 0
- for contig in contig_objects2:
- if contig.position >= max_pos:
- linking_contig2 = contig
- max_pos = contig.position
-
- min_pos = sys.maxint
- for contig in contig_objects1:
- if contig.position <= min_pos:
- linking_contig1 = contig
- min_pos = contig.position
- linking_contig1.links[linking_contig2.name] = nr_links
- linking_contig2.links[linking_contig1.name] = nr_links
-
-
- elif side1 == 'R' and side2 == 'R':
- max_pos = 0
- for contig in contig_objects1:
- if contig.position >= max_pos:
- linking_contig1 = contig
- max_pos = contig.position
-
- max_pos = 0
- for contig in contig_objects2:
- if contig.position >= max_pos:
- linking_contig2 = contig
- max_pos = contig.position
- linking_contig1.links[linking_contig2.name] = nr_links
- linking_contig2.links[linking_contig1.name] = nr_links
-
-
- elif side1 == 'L' and side2 == 'L':
- min_pos = sys.maxint
- for contig in contig_objects1:
- if contig.position <= min_pos:
- linking_contig1 = contig
- min_pos = contig.position
- min_pos = sys.maxint
- for contig in contig_objects2:
- if contig.position <= min_pos:
- linking_contig2 = contig
- min_pos = contig.position
-
- linking_contig1.links[linking_contig2.name] = nr_links
- linking_contig2.links[linking_contig1.name] = nr_links
diff --git a/external/gatb-minia-pipeline/BESST/BESST/Parameter.py b/external/gatb-minia-pipeline/BESST/BESST/Parameter.py
deleted file mode 100644
index a9dda8d29655b34101b3274e68d4ad71e155c9f6..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/Parameter.py
+++ /dev/null
@@ -1,127 +0,0 @@
-'''
- Created on Mar 31, 2012
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-
-class parameter(object):
- '''
- classdocs
- '''
- def __init__(self, parameter_mean_coverage=None, parameter_std_dev_coverage=None,
- parameter_mean_ins_size=None , parameter_std_dev_ins_size=None,
- parameter_output_directory=None, parameter_bamfile=None,
- parameter_read_len=None,
- parameter_ins_size_threshold=None, parameter_contigfile=None,
- parameter_edgesupport=None, parameter_contig_threshold=None,
- parameter_scaffold_indexer=0, parameter_first_lib=None,
- parameter_cov_cutoff=None, parameter_tot_assembly_length=None,
- parameter_current_N50=None, parameter_current_L50=None,
- parameter_hapl_ratio=None, parameter_hapl_threshold=None,
- parameter_detect_haplotype=None, parameter_detect_duplicate=None,
- parameter_gff_file=None, parameter_information_file=None,
- parameter_extend_paths=None, FASTER_ILP=None,
- parameter_development=None, parameter_plots=None, parameter_path_threshold=None,
- path_gaps_estimated =0, parameter_gap_estimations = [],
- contamination_mean=None, contamination_stddev = None, contamination_ratio=0,
- no_score=None, orientation = None, contig_index= None,
- score_cutoff = None, max_extensions = None, NO_ILP=None, print_scores=None,pass_number=None):
-
-
-
- # Library information
- self.mean_ins_size = parameter_mean_ins_size
- self.std_dev_ins_size = parameter_std_dev_ins_size
-
- # Contig information
- self.contig_index = contig_index
- # Algorithm parameters
- self.score_cutoff = score_cutoff
- self.max_extensions = max_extensions
- # Assembly information
- # Algorithm information
- # Output information
- self.mean_coverage = parameter_mean_coverage
- self.std_dev_coverage = parameter_std_dev_coverage
- self.output_directory = parameter_output_directory
- self.bamfile = parameter_bamfile
- self.read_len = parameter_read_len
- self.ins_size_threshold = parameter_ins_size_threshold
- self.contigfile = parameter_contigfile
- self.edgesupport = parameter_edgesupport
- self.contig_threshold = parameter_contig_threshold
- self.scaffold_indexer = parameter_scaffold_indexer
- self.first_lib = parameter_first_lib
- self.cov_cutoff = parameter_cov_cutoff
- self.tot_assembly_length = parameter_tot_assembly_length
- self.current_N50 = parameter_current_N50
- self.current_L50 = parameter_current_L50
- self.hapl_ratio = parameter_hapl_ratio
- self.hapl_threshold = parameter_hapl_threshold
- self.detect_haplotype = parameter_detect_haplotype
- self.detect_duplicate = parameter_detect_duplicate
- self.gff_file = parameter_gff_file
- self.information_file = parameter_information_file
- self.extend_paths = parameter_extend_paths
- self.development = parameter_development
- self.plots = parameter_plots
- self.path_threshold = parameter_path_threshold
- self.no_score = no_score
- self.orientation = orientation
- self.pass_number = pass_number
- # debugging and logging
- self.print_scores = print_scores
-
-
- # related to gap distances
- self.path_gaps_estimated = path_gaps_estimated
- self.gap_estimations = parameter_gap_estimations
-
- # If MP library (PE contamination)
- self.contamination_ratio = contamination_ratio
- self.contamination_mean = contamination_mean
- self.contamination_stddev = contamination_stddev
- self.NO_ILP = NO_ILP
- self.FASTER_ILP = FASTER_ILP
-
-class counters(object):
- def __init__(self, param_count=None, param_non_unique=None, param_non_unique_for_scaf=None,
- param_nr_of_duplicates=None, param_prev_obs1=None, param_prev_obs2=None,
- param_reads_with_too_long_insert=None):
-
- self.count = param_count
- self.non_unique = param_non_unique
- self.non_unique_for_scaf = param_non_unique_for_scaf
- self.nr_of_duplicates = param_nr_of_duplicates
- self.prev_obs1 = param_prev_obs1
- self.prev_obs2 = param_prev_obs2
- self.reads_with_too_long_insert = param_reads_with_too_long_insert
-
-#
-#def MemoryUsage():
-# percent_usage = subprocess.Popen("ps -v | grep 'python Main.py' | awk '{sum+=$12} END {print sum}'",
-# shell=True,
-# stdout=subprocess.PIPE,
-# )
-# stdout_list = percent_usage.communicate()[0]
-# print 'Percentage of memory occupied by BESST from total memory: ', stdout_list
-# return()
-
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/Scaffold.py b/external/gatb-minia-pipeline/BESST/BESST/Scaffold.py
deleted file mode 100644
index ef08900056ed96fdbb79923f2702149d58856c90..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/Scaffold.py
+++ /dev/null
@@ -1,38 +0,0 @@
-'''
- Created on Sep 29, 2011
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-
-class scaffold(object):
- '''
- classdocs
- '''
-
- __slots__ = ('name', 'contigs', 's_length')
- def __init__(self, scaffold_name, scaffold_contigs, scaffold_length):
- '''
- Constructor
- '''
- self.name = scaffold_name # String name
- self.contigs = scaffold_contigs # list of contig objects that are ordered as they should be placed in the scaffold
- self.s_length = scaffold_length # integer of total length of the scaffold
-
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/bam_parser.py b/external/gatb-minia-pipeline/BESST/BESST/bam_parser.py
deleted file mode 100644
index ff3be4069a2355c77c343c40dfa1311c1a69ff0d..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/bam_parser.py
+++ /dev/null
@@ -1,205 +0,0 @@
-import os
-import sys
-import pysam
-
-##
-# Opens a .bam or .sam file and returns the file
-# object.
-#
-# @param bam_file_path Path to the .bam or .sam.
-#
-# @return File object for .bam or .sam.
-#
-def open_bam_file(bam_file_path):
- bam_file_name, bam_file_ext = os.path.splitext(bam_file_path)
- if bam_file_ext == ".bam":
- return pysam.Samfile(bam_file_path, 'rb')
- elif bam_file_ext == ".sam":
- return pysam.Samfile(bam_file_path, 'r')
- else:
- return IOError("open_bam_file: File must be either .bam or .sam.")
-
-def is_proper_aligned_unique_innie(read):
- return (read.is_reverse and not read.mate_is_reverse and read.is_read2 and read.tlen < 0 and read.rname == read.mrnm) or \
- (not read.is_reverse and read.mate_is_reverse and read.is_read2 and read.tlen > 0 and read.rname == read.mrnm ) \
- and not read.mate_is_unmapped and read.mapq > 10 and not read.is_secondary
-def is_proper_aligned_unique_outie(read):
- return (read.is_reverse and not read.mate_is_reverse and read.is_read2 and read.tlen > 0 and read.rname == read.mrnm) or \
- (not read.is_reverse and read.mate_is_reverse and read.is_read2 and read.tlen < 0 and read.rname == read.mrnm ) \
- and not read.mate_is_unmapped and read.mapq > 10 and not read.is_secondary
-
-def is_unique_read_link(read):
- # if not read.is_unmapped and not read.mate_is_unmapped and read.rname != read.mrnm \
- # and read.opt('XT')=='U' and not read.is_secondary and read.rlen != read.alen:
- # print read
- return not read.is_unmapped and not read.mate_is_unmapped and read.rname != read.mrnm \
- and read.mapq > 10 and not read.is_secondary
-
-
-### BOWTIE ####
-def proper_unique_alignment_innie_bowtie(read1,read2):
- unique1 = not read1.is_unmapped and not read1.is_secondary
- unique2 = not read2.is_unmapped and not read2.is_secondary
- is_innie = not read1.is_reverse and read2.is_reverse and read1.pos < read2.pos \
- or read1.is_reverse and not read2.is_reverse and read1.pos > read2.pos
- return unique1 and unique2 and is_innie
-
-def proper_unique_alignment_outie_bowtie(read1,read2):
- unique1 = not read1.is_unmapped and not read1.is_secondary
- unique2 = not read2.is_unmapped and not read2.is_secondary
- is_outie = read1.is_reverse and not read2.is_reverse and read1.pos < read2.pos \
- or not read1.is_reverse and read2.is_reverse and read1.pos > read2.pos
- return unique1 and unique2 and is_outie
-
-def unique_link_alignment_bowtie(read1,read2):
- unique1 = not read1.is_unmapped and not read1.is_secondary
- unique2 = not read2.is_unmapped and not read2.is_secondary
- return unique1 and unique2
-
-##############
-
-def get_mp_observation(read1, read2, ctg_len1, ctg_len2):
- if not read1.is_reverse:
- obs1 = read1.pos + read1.qlen
- else:
- obs1 = ctg_len1 - read1.pos
-
- if not read2.is_reverse:
- obs2 = read2.pos + read2.qlen
- else:
- obs2 = ctg_len2 - read2.pos
- return obs1, obs2
-
-def get_pe_observation(read1, read2, ctg_len1, ctg_len2):
- if read1.is_reverse:
- obs1 = read1.pos + read1.qlen
- else:
- obs1 = ctg_len1 - read1.pos
-
- if read2.is_reverse:
- obs2 = read2.pos + read2.qlen
- else:
- obs2 = ctg_len2 - read2.pos
- return obs1, obs2
-
-class BamParser(object):
- """docstring for BamParser"""
- def __init__(self, bam_file,bam_path2 = None):
- super(BamParser, self).__init__()
- self.bam_file = open_bam_file(bam_file)
- if bam_path2:
- self.bam_file2 = open_bam_file(bam_path2)
- self.contig_lengths = dict(zip(self.bam_file.references,self.bam_file.lengths))
-
- def proper_aligned_unique_pairs(self,aligner, samples=2**32):
- nr_samples = 0
- if aligner == 'bwa' or aligner == 'bwa_mem':
- for ref, length in sorted(zip(self.bam_file.references,self.bam_file.lengths),key = lambda x: x[1], reverse = True):
- try:
- iter_ = self.bam_file.fetch(ref)
- except ValueError:
- sys.stderr.write('Need indexed bamfiles, index file should be located in the same directory as the BAM file\nterminating..\n')
- sys.exit(0)
- for read in iter_:
- if read.is_read2 and is_proper_aligned_unique_innie(read):
- nr_samples += 1
- yield 'innie',read
- elif read.is_read2 and is_proper_aligned_unique_outie(read):
- nr_samples += 1
- yield 'outie',read
-
- if nr_samples >= samples:
- break
- self.bam_file.seek(0)
-
-
- elif aligner == 'bowtie':
- ctgs_largest_first = [ref for ref, length in sorted(zip(self.bam_file.references,self.bam_file.lengths), key = lambda x: x[1], reverse = True)]
- long_ctgs = set(ctgs_largest_first[:10])
- for read1,read2 in zip(self.bam_file,self.bam_file2):
- assert read1.qname == read2.qname
- same_ref = read1.rname == read2.rname
- if same_ref and proper_unique_alignment_innie_bowtie(read1,read2):
- if not self.bam_file.getrname( read1.tid) in long_ctgs and not self.bam_file2.getrname(read2.tid) in long_ctgs:
- continue
- nr_samples += 1
- read1.tlen = abs(read1.pos - read2.pos) + read1.rlen
- yield 'innie',read1
- elif same_ref and proper_unique_alignment_outie_bowtie(read1,read2):
- if not self.bam_file.getrname( read1.tid) in long_ctgs and not self.bam_file2.getrname(read2.tid) in long_ctgs:
- continue
- nr_samples += 1
- read1.tlen = abs(read1.pos - read2.pos) + 2*read1.rlen
- yield 'outie',read1
-
- if nr_samples >= samples:
- break
- self.bam_file.seek(0)
-
- def aligned_reads(self,aligner):
- if aligner == 'bwa' or aligner == 'bwa_mem':
- for read in self.bam_file:
- if not read.is_unmapped:
- yield read
- self.bam_file.seek(0)
- elif aligner == 'bowtie':
- for read1,read2 in zip(self.bam_file,self.bam_file2):
- if not read1.is_unmapped and not read2.is_unmapped:
- yield read1,read2
- elif not read1.is_unmapped:
- yield read1,False
- elif not read2.is_unmapped:
- yield False, read2
-
- def unique_reads_on_different_references(self, aligner):
- read_pairs = {}
- if aligner == 'bwa_mem':
- for read in self.bam_file:
- if is_unique_read_link(read):
- #tmp for tests:
- #print read.qname[:-1]
- #print read_pairs
- if read.qname in read_pairs:
- #print 'lol'
- #read2 = read_pairs[read.qname]
- #if read.tid == read2.tid:
- yield read, read_pairs[read.qname]
- #else:
- # pass
- del read_pairs[read.qname]
- else:
- read_pairs[read.qname] = read
-
-
-
- elif aligner == 'bwa':
- pass
-
- elif aligner == 'bowtie':
- for read1,read2 in zip(self.bam_file,self.bam_file2):
- assert read1.qname == read2.qname
- same_ref = read1.rname == read2.rname
- if not same_ref and unique_link_alignment_bowtie(read1,read2):
- read1.tlen = abs(read1.pos - read2.pos) + read1.rlen
- yield read1, read2
- elif not same_ref and unique_link_alignment_bowtie(read1,read2):
- read1.tlen = abs(read1.pos - read2.pos) + 2*read1.rlen
- yield read1, read2
-
- self.bam_file.seek(0)
-
- def long_reads_for_coverage(self):
- pass
- def long_reads_scaffold_links(self):
- pass
-
-def main(path):
- for read in BamParser(path).reads_for_coverage():
- if read.qlen != 100:
- #print read.tags
- print read.qlen
- #print read.opt('XT')
-
-
-if __name__ == '__main__':
- main(sys.argv[1])
diff --git a/external/gatb-minia-pipeline/BESST/BESST/decide_approach.py b/external/gatb-minia-pipeline/BESST/BESST/decide_approach.py
deleted file mode 100644
index ac5443ffeecd8037411dc5bcc1bf2d98452096b1..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/decide_approach.py
+++ /dev/null
@@ -1,24 +0,0 @@
-import sys
-
-def NX(x,lengths):
- lengths.sort(reverse=True)
- N100 = sum(lengths)
- stop = N100/ (100/float(x))
- curr_sum = 0
- for length in lengths:
- curr_sum += length
- if curr_sum >= stop:
- return length
-
-def decide_scaffolding_procedure(Scaffolds,small_scaffolds, param):
- lengths_long = map(lambda x: Scaffolds[x].s_length, Scaffolds)
- lengths_short = map(lambda x: small_scaffolds[x].s_length, small_scaffolds)
- lengths = lengths_long + lengths_short
- N60 = NX(60,lengths)
- if N60 < param.ins_size_threshold and param.extend_paths:
- param.no_score = True
- param.contig_threshold = N60 - 1
- sys.stdout.write('Too fragmented assembly (given the insert size of the library)\
- for statistical scoring. Proceding with path finding.')
- else:
- pass
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/__init__.py b/external/gatb-minia-pipeline/BESST/BESST/diploid/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/get_haplotype_regions.py b/external/gatb-minia-pipeline/BESST/BESST/diploid/get_haplotype_regions.py
deleted file mode 100644
index 0b04196d3675a63eda6f8f94e6b98b3820d0efec..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid/get_haplotype_regions.py
+++ /dev/null
@@ -1,356 +0,0 @@
-'''
-Created on Jun 17, 2013
-
-@author: ksahlin
-'''
-'''
-Created on Mar 15, 2013
-
-@author: ksahlin
-'''
-
-import os
-import sys
-import time
-from collections import defaultdict
-import itertools
-from operator import itemgetter
-import gc
-
-import networkx as nx
-
-import smith_waterman
-import wrapper_sw
-import output_contigs
-
-
-
-# generate the reverse complement of a sequence
-def reverse_complement(string):
- #rev_nuc = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'N':'N', 'X':'X'}
- # Modified for Abyss output
- rev_nuc = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'a':'t', 'c':'g', 'g':'c', 't':'a', 'N':'N', 'X':'X', 'n':'n', 'Y':'R', 'R':'Y', 'K':'M', 'M':'K', 'S':'S', 'W':'W', 'B':'V', 'V':'B', 'H':'D', 'D':'H', 'y':'r', 'r':'y', 'k':'m', 'm':'k', 's':'s', 'w':'w', 'b':'v', 'v':'b', 'h':'d', 'd':'h'}
-
- rev_comp = ''.join([rev_nuc[nucl] for nucl in reversed(string)])
- return(rev_comp)
-
-def create_kmers(k, m, sequence, acc, k_mer_hash):
- #get length of contig
- read_length = len(sequence)
- # k_mer_hash =(contig accession, beginning/end, forw/rev)
- # beginning = 0
- # end = 1
- # forward = 0
- # reverse complement = 1
-
- contig_begin = sequence[:k ]
- contig_end = sequence[read_length - k:]
-
- # iterate over all m-mers in the k subsequence of the contig
- for i in range(len(contig_begin) - m + 1):
- # fill up k-mer hash table with k-mer as key and
- # tuple (contig accession, beginning/end, forw/rev) as value
- k_mer_hash[contig_begin[i : m + i]].append((acc, 0 , 0))
- k_mer_hash[reverse_complement(contig_begin[i : m + i])].append((acc, 0 , 1))
- k_mer_hash[contig_end[i : m + i]].append((acc, 1 , 0))
- k_mer_hash[reverse_complement(contig_end[i : m + i])].append((acc, 1 , 1))
- # fill up contig hash table with contig accession as key and
- # k-mer hash table (contig accession, beginning/end, forw/rev) as value
-
- return()
-
-def get_kmer_index(contigs, k, m):
- k_mer_hash = defaultdict(list)
- cntr = 0
- for accession, sequence in contigs.iteritems():
- cntr += 1
- create_kmers(k, m, sequence, accession, k_mer_hash)
- if cntr % 100000 == 0:
- print 'Creating k-mers of ', cntr, ' contigs.'
- return(k_mer_hash)
-
-# given an iterable of pairs return the key corresponding to the greatest value
-def argmax(pairs):
- return max(pairs, key=itemgetter(1))[0]
-
-# given an iterable of values return the index of the greatest value
-def argmax_index(values):
- return argmax(enumerate(values))
-
-def is_haplotype_region(contigs, haplotypes, similarity_threshold):
-
- # Check if only one contig on this side, it should then be merged if
- # the other region is haplotypic. We therefore return True
-
- if len(haplotypes) == 1:
- return(1)
-
- # Check if no contig on this side, this could be the case if e.g. low coverage on one s
- # side. We want to merge the other side anyway if it is similar. We therefore return True
- if len(haplotypes) == 0:
- print 'No contig on one side!'
- return(1)
- seqs = itertools.combinations(haplotypes, 2)
- score = 0
- nr_comparisons = 0
- nr_matching = 0
- for pair in seqs:
- nr_comparisons += 1
- len_ctg1 = len(contigs[pair[0][0]])
- len_ctg2 = len(contigs[pair[1][0]])
- if pair[0][2] == 1:
- contig1 = reverse_complement(contigs[pair[0][0]])
- else:
- contig1 = contigs[pair[0][0]]
-
- if pair[1][2] == 1:
- contig2 = reverse_complement(contigs[pair[1][0]])
- else:
- contig2 = contigs[pair[1][0]]
-
- score, max_i, max_j = wrapper_sw.wrap_sw(contig1, contig2, 0, 0)
-
- #print score, max_i, max_j
-
- ## TODO:
- # Wrong in formula!! need too make sure that we start aligning from the similar k-mer
- # and then take min(max_i, max_j) or max(....)?? Figure out
- procent_similarity = score / float(max(min(max_i, max_j), min(len_ctg1, len_ctg2))) #float(min(max_i, max_j, len_ctg1, len_ctg2))
- print 'Score', procent_similarity, 'length alignment:', float(min(max_i, max_j, len_ctg1, len_ctg2)), 'length ctgs:', len_ctg1, len_ctg2
- if procent_similarity > similarity_threshold:
- nr_matching += 1
-
- if nr_matching == nr_comparisons:
- return(1)
- else:
- return()
-
-def graph_updater(connectedness_graph, contigs, nodes, remove_nodes):
- # One side might be empty this is a special case. (see comments in "is_haplotype_region" function)
- if len(nodes) == 0:
- return False
-
-
- # Remove all reverse complement nodes (they are redundant) after we
- # have classified the region (they are removed after the loop in search_regions)
- nodes_rev_comp = map(lambda x: (x[0], x[1], 1 - x[2]) , nodes)
- remove_nodes.update(nodes_rev_comp)
- longest_contig_index = argmax_index([len(contigs[ctg[0]]) for ctg in nodes])
- hapl_lengths = map(lambda x: len(contigs[x[0]]), nodes)
-
- # Need to pick the longest haplotype. This is a corner case where
- # there are at least two longest contigs. We then need to stick to one consistently
- if hapl_lengths.count(max(hapl_lengths)) > 1:
- #print 'OMGGGGG Same length of haplotypes (need to choose one):'
- #print nodes
- pass
-
- index_ = 0
- for hapl in nodes:
- if len(contigs[hapl[0]]) == max(hapl_lengths):
- try:
- connectedness_graph.node[hapl]['r']
- except KeyError:
- longest_contig_index = index_
- index_ += 1
-
-
- #print 'INDEX:', longest_contig_index
- for index, ctg in enumerate(nodes):
- if index != longest_contig_index:
- connectedness_graph.node[ctg]['r'] = 1
-
- # need to update other end of contig as well
- # if it was added to the k-mer connection graph
- # note: not all k-mers of contig ends need to have
- # multiple hits. If only one hit, it is not added.
- # therefore, not all contig ends might be represented in
- # connectedness_graph
- try:
- connectedness_graph.node[(ctg[0], 1 - ctg[1], 1)]['r'] = 1
- except KeyError:
- pass
- try:
- connectedness_graph.node[(ctg[0], 1 - ctg[1], 0)]['r'] = 1
- except KeyError:
- pass
-
- else:
- ctg_to_join = ctg
-
-
-
-
- return(ctg_to_join)
-
-
-def haplotype_detect(connectedness_graph, contigs, nodes, similarity_threshold, remove_nodes):
-
- ## check to see that node has not been merged previously
- #if not all([ctg[0] in contigs for ctg in nodes]):
- # return(0)
-
- ctg_left, ctg_right = None, None
- before_kmer = filter(lambda x: (x[1] + x[2]) % 2 == 1, nodes)
- if is_haplotype_region(contigs, before_kmer, similarity_threshold):
- ctg_left = graph_updater(connectedness_graph, contigs, before_kmer, remove_nodes)
-
-
-
- after_kmer = filter(lambda x: (x[1] + x[2]) % 2 == 0, nodes)
- if is_haplotype_region(contigs, after_kmer, similarity_threshold):
- ctg_right = graph_updater(connectedness_graph, contigs, after_kmer, remove_nodes)
-
- if ctg_right:
- for nbr in connectedness_graph.neighbors(ctg_right):
- if nbr in nodes:
- connectedness_graph[ctg_right][nbr]['a'] = 1
-
- if ctg_left:
- for nbr in connectedness_graph.neighbors(ctg_left):
- if nbr in nodes:
- connectedness_graph[ctg_left][nbr]['a'] = 1
-
- if ctg_left and ctg_right:
- if connectedness_graph.has_edge(ctg_left, ctg_right):
- connectedness_graph[ctg_left][ctg_right]['m'] = 1
- else:
- connectedness_graph.add_edge(ctg_left, ctg_right, m=1)
-
-
-
-
- # Save information of what contigs that should be saved,
- # what contigs that shoud be removed and what contigs that
- # should be "joined" with SW. Also store the coordinates for merging
-
-
- return()
-
-def search_regions(k_mer_hash, contigs, similarity_threshold):
-
- # create graph with connections
- cntr = 0
- cntr2 = 0
- #cntr3 = 0
- connectedness_graph = nx.Graph()
- print 'Number of m-mers in m-mer hash table: ', len(k_mer_hash)
-
- # We will not look at nodes with more than 10 triangles = clique < 6 nodes =
- filtered_list = filter(lambda x: 1 < len(x) < 6, k_mer_hash.values())
- #print filtered_list
- for ctgs in filtered_list:
- cntr2 += 1
- #cntr3 += 1
- #if cntr3 >= 7000000:
- # break
- if cntr2 % 100000 == 0:
- print cntr2, ' items have been treated.'
- #print k_mer
- if len(ctgs) > 1:
- cntr += 1
- # print 'here'
- connections = itertools.combinations(ctgs, 2)
- connectedness_graph.add_edges_from(connections)
-
- if cntr % 10000 == 0:
- print 'Constructed graph from ', cntr, ' k-mers.', 'nr ctgs for k-mer: ', len(ctgs)
- #print 'Total nr of nodes: ', len(connectedness_graph.nodes())
- #print 'Total nr of edges: ', len(connectedness_graph.edges())
-
- # Look for interesting (looking like split haplotypes) regions in connectedness_graph
- interesting_regions = set([1, 3, 6])
- visited_nodes = set()
- remove_nodes = set()
- cntr = 0
- print 'len', len(contigs)
- for node in connectedness_graph:
- # We modify (remove nodes) as we go so we need to check if the node is still there
- if node not in visited_nodes:
- # visited nodes are both the actual visited triangle and its reverse complement
- if nx.algorithms.triangles(connectedness_graph, node) in interesting_regions:
- nodes = connectedness_graph.neighbors(node) + [node]
- # add speed up here, mark visited nodes / triangles and there reverse complements
- nodes_rev_comp = map(lambda x: (x[0], x[1], 1 - x[2]) , nodes)
- #print nodes , nodes_rev_comp
- visited_nodes.update(nodes)
- visited_nodes.update(nodes_rev_comp)
- cntr += 1
- if cntr % 10 == 0:
- print cntr
- #if cntr > 20:
- # break
- haplotype_detect(connectedness_graph, contigs, nodes, similarity_threshold, remove_nodes)
-
-
-
- print 'REMOVED:', len(remove_nodes)
-
- # Remove all reverse complement nodes to regions that have been classified as haplotypic regions
- connectedness_graph.remove_nodes_from(remove_nodes)
-
-
- # Remove all connections that did not pass as haplotyic regions
- # They should have no key attributes
- rmv_edges = []
- for edge in connectedness_graph.edges_iter():
- if not connectedness_graph[edge[0]][edge[1]]:
- rmv_edges.append(edge)
- connectedness_graph.remove_edges_from(rmv_edges)
-
- rmv_nodes = []
- for node in connectedness_graph:
- if connectedness_graph.neighbors(node) == 0:
- rmv_nodes.append(node)
- connectedness_graph.remove_nodes_from(rmv_nodes)
-
- for node in connectedness_graph:
- try:
- connectedness_graph.node[node]['r']
- except KeyError:
- connectedness_graph.node[node]['r'] = 0
-
-
- print 'nr nodes left:', len(connectedness_graph.nodes())
- print 'nr edges left:', len(connectedness_graph.edges())
-
- return(connectedness_graph)
-
-
-def main(output_dir, contigs, k, m, similarity_threshold):
- # start timing
- start_time = time.time()
- k_mer_hash = get_kmer_index(contigs, k, m)
- print 'Done with m-mer graph.'
- connectedness_graph = search_regions(k_mer_hash, contigs, similarity_threshold)
- output_contigs.generate_fasta(connectedness_graph, contigs, output_dir, k)
- # stop timing
- end_time = time.time()
- # print timing
- print "time:", end_time - start_time
- return()
-
-if __name__ == '__main__':
- import argparse
- parser = argparse.ArgumentParser(description='Outputs k-mers for a given input sequence')
- parser.add_argument('k', type=int, help='assembly k-mer size.')
- parser.add_argument('m', type=int, help='Length of matching seeds (m-mer size) <= k-mer.')
- parser.add_argument('t', type=float, default=0.7, help='Procent similarity threshold (number between 0 and 1)')
- #parser.add_argument('sequence', type=str, help='Sequence to split into k-mers')
- args = parser.parse_args()
- contigs = {'ctg1' : 'TTTGCGCGTCGTGCTGCAAGGTTGTTAC', 'ctg2' : 'AAGGTTGTTACTTTTTTTGGGGGGTTTTGAAACAACCAA',
- 'ctg3' : 'AAGGTTGTTACTCGTAAATAAAACAACCAA', 'ctg4' : 'AAACAACCAAGGTGTGGTGTAGTCGTCGTGTCGTC'}
- # start timing
- start_time = time.time()
-
- k_mer_hash = get_kmer_index(contigs, args.k, args.m)
- search_regions(k_mer_hash, contigs, args.t)
-
-
- # stop timing
- end_time = time.time()
-
-
- # print timing
- print "time:", end_time - start_time
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/lib/swmodule b/external/gatb-minia-pipeline/BESST/BESST/diploid/lib/swmodule
deleted file mode 100755
index 463899487e55b1bdc830598d76bb6c0e637e5f0b..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/BESST/BESST/diploid/lib/swmodule and /dev/null differ
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/lib/swmodule.cpp b/external/gatb-minia-pipeline/BESST/BESST/diploid/lib/swmodule.cpp
deleted file mode 100644
index c51dfe0a68d2dfd9393858088dd552f58f566ae1..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid/lib/swmodule.cpp
+++ /dev/null
@@ -1,340 +0,0 @@
-#include <iostream>
-#include <fstream>
-#include <cstdlib>
-#include <string>
-#include <cmath>
-#include <sys/time.h>
-#include <string.h>
-using namespace std;
-
-double similarity_score(char a,char b);
-double find_array_max(double array[],int length);
-void insert_at(char arr[], int n, int idx, char val);
-void checkfile(int open, char filename[]);
-string read_sequence(ifstream& f);
-
-
-double mu;
-double delta;
-
-typedef struct {
-int score;
-int max_i;
-int max_j;
-} Coordinate;
-
-extern "C"
-
-int SW(char *seq_a_, char *seq_b_, Coordinate *result);
-
-int main(int argc,char *argv[]){
- char *seq_a = (char *) malloc( 1500 );
- char *seq_b = (char *) malloc( 1500 );
-
- memset( seq_a, 'A', 1500 );
- memset( seq_b, 'G', 1500 );
- seq_a[ 1499 ] = '\0';
- seq_b[ 1499 ] = '\0';
-
- Coordinate res;
- SW( seq_a, seq_b, &res );
-}
-
-
-int SW(char *seq_a_, char *seq_b_, Coordinate *result){
-
- string seq_a(seq_a_);
- string seq_b(seq_b_);
-
-/* // read info from arguments
- if(argc!=6){
- cout<<"Give me the proper number of input arguments:"<<endl<<"1 : mu"<<endl;
- cout<<"2 : delta"<<endl<<"3 : filename sequence A"<<endl<<"4 : filename sequence B"<<endl;
- cout<<"5 : maximal length N of sequences"<<endl;exit(1);
- }*/
- double mu,delta;
- mu = 0;
- delta = 0;
-/* // atof(argv[2]);
- /////////////////////////////////
- // give it the filenames
- char *nameof_seq_a = argv[3];
- char *nameof_seq_b = argv[4];
- int N_max = 1000; //atoi(argv[5]);
- string seq_a,seq_b;
- */
-/* // read the sequences into two vectors:
- ifstream stream_seq_b; // first define the input-streams for seq_a and seq_b
- stream_seq_b.open(nameof_seq_b); // the same for seq_b
- checkfile(! stream_seq_b,nameof_seq_b);
- seq_b = read_sequence(stream_seq_b);
- ifstream stream_seq_a;
- stream_seq_a.open(nameof_seq_a); // open the file for input
- checkfile(! stream_seq_a,nameof_seq_a); // check, whether the file was opened successfully
- seq_a = read_sequence(stream_seq_a);
-
- */
- // string s_a=seq_a,s_b=seq_b;
- int N_a = seq_a.length(); // get the actual lengths of the sequences
- int N_b = seq_b.length();
- //cout << N_b << " "<<N_a <<endl;
-
- ////////////////////////////////////////////////
-
- // initialize H
- double *H_cur_row = (double *) malloc( sizeof( double ) * (N_b + 1) );
- double *H_prev_row = (double *) malloc( sizeof( double ) * (N_b + 1) );
-
- // initialize final storage to get length of alignment
- double *Last_row = (double *) malloc( sizeof( double ) * (N_b + 1) );
- double *Last_col = (double *) malloc( sizeof( double ) * (N_a + 1) );
-
- for(int i=0;i<=N_b;i++){
- H_cur_row[i]=0.;
- H_prev_row[i]=0.;
- Last_row[i]=0.;
- }
-
- for(int i=0;i<=N_a;i++){
- Last_col[i]=0.;
- }
-
-/* double **H = (double **) malloc( sizeof( double * ) * (N_a + 1) );
- for(int i=0; i<=N_a; i++)
- {
- H[ i ] = (double *) malloc( sizeof( double ) * (N_b + 1) );
- }
-
- for(int i=0;i<=N_a;i++){
- for(int j=0;j<=N_b;j++){
- H[i][j]=0.;
- }
- }*/
-
- double temp[3];
-// int I_i[N_a+1][N_b+1],I_j[N_a+1][N_b+1]; // Index matrices to remember the 'path' for backtracking
-
- char chr1;
- char chr2;
- for(int i=1;i<=N_a;i++){
- for(int j=1;j<=N_b;j++){
- chr1 = seq_a.at(i-1);
- chr2 = seq_b.at(j-1);
- temp[0] = H_prev_row[j-1]+similarity_score(chr1,chr2); //H[i-1][j-1]+similarity_score(chr1,chr2);
- temp[1] = H_prev_row[j]-delta; //H[i-1][j]-delta;
- temp[2] = H_cur_row[j-1]-delta; // H[i][j-1]-delta;
- H_cur_row[j] = find_array_max(temp,3);//H[i][j] = find_array_max(temp,3);
- if(j ==N_b){
- Last_col[i] = H_cur_row[j];
- }
-
- }
-
- //We only keep track of two rows in the scoring matrix. When
- // we advance one row we update the current row to be the
- // new previous row. The old previous row is written over by zeros
-/* for(int k=0;k<=N_b;k++){
- cout << "previous: "<< H_prev_row[k] <<endl;
- cout << "Current: "<< H_cur_row[k] <<endl;
- }*/
-
- swap( H_cur_row, H_prev_row );
-
- for(int j=0;j<=N_b;j++){
- H_cur_row[j]=0.;
- }
-
- }
-
- for(int j=0;j<=N_b;j++){
- Last_row[j]=H_prev_row[j];
- }
-
-
-
-
-/*
- // here comes the actual algorithm
- char chr1;
- char chr2;
- for(int i=1;i<=N_a;i++){
- for(int j=1;j<=N_b;j++){
- chr1 = seq_a.at(i-1);
- chr2 = seq_b.at(j-1);
- temp[0] = H[i-1][j-1]+similarity_score(chr1,chr2);
- temp[1] = H[i-1][j]-delta;
- temp[2] = H[i][j-1]-delta;
- //temp[3] = 0.;
- H[i][j] = find_array_max(temp,3);
- switch(ind){
- case 0: // score in (i,j) stems from a match/mismatch
- I_i[i][j] = i-1;
- I_j[i][j] = j-1;
- break;
- case 1: // score in (i,j) stems from a deletion in sequence A
- I_i[i][j] = i-1;
- I_j[i][j] = j;
- break;
- case 2: // score in (i,j) stems from a deletion in sequence B
- I_i[i][j] = i;
- I_j[i][j] = j-1;
- break;
- case 3: // (i,j) is the beginning of a subsequence
- I_i[i][j] = i;
- I_j[i][j] = j;
- break;
- }
- }
- }
-
- // Print the matrix H to the console
- cout<<"**********************************************"<<endl;
- cout<<"The scoring matrix is given by "<<endl<<endl;
- for(int i=1;i<=N_a;i++){
- for(int j=1;j<=N_b;j++){
- cout<<H[i][j]<<" ";
- }
- cout<<endl;
- }*/
-
- // search H for the maximal score TODO: Only on the last row and column (local alignment)
- double H_max = 0.;
- int i_max=0,j_max=0;
- for(int i=1;i<=N_a;i++){
- if(Last_col[i]>H_max){
- H_max = Last_col[i];
- i_max = i;
- j_max = N_b;
- }
- }
- for(int j=1;j<=N_b;j++){
- if(Last_row[j]>H_max){
- H_max = Last_row[j];
- i_max = N_a;
- j_max = j;
- }
- }
-
-
-/* for(int i=1;i<=N_a;i++){
- for(int j=1;j<=N_b;j++){
- if(H[i][j]>H_max){
- H_max = H[i][j];
- i_max = i;
- j_max = j;
- }
- }
- }*/
- result->score = H_max;
- result->max_i = i_max;
- result->max_j = j_max;
-
-
- //cout<<H_max<<endl;
-/*
- // Backtracking from H_max
- int current_i=i_max,current_j=j_max;
- int next_i=I_i[current_i][current_j];
- int next_j=I_j[current_i][current_j];
- int tick=0;
- char consensus_a[N_a+N_b+2],consensus_b[N_a+N_b+2];
-
- while(((current_i!=next_i) || (current_j!=next_j)) && (next_j!=0) && (next_i!=0)){
- if(next_i==current_i) consensus_a[tick] = '-'; // deletion in A
- else consensus_a[tick] = seq_a.at(current_i-1); // match/mismatch in A
-
- if(next_j==current_j) consensus_b[tick] = '-'; // deletion in B
- else consensus_b[tick] = seq_b.at(current_j-1); // match/mismatch in B
-
- current_i = next_i;
- current_j = next_j;
- next_i = I_i[current_i][current_j];
- next_j = I_j[current_i][current_j];
- tick++;
- }
-
-
- // Output of the consensus motif to the console
- cout<<endl<<"***********************************************"<<endl;
- cout<<"The alignment of the sequences"<<endl<<endl;
- for(int i=0;i<N_a;i++){cout<<seq_a[i];}; cout<<" and"<<endl;
- for(int i=0;i<N_b;i++){cout<<seq_b[i];}; cout<<endl<<endl;
- cout<<"is for the parameters mu = "<<mu<<" and delta = "<<delta<<" given by"<<endl<<endl;
- for(int i=tick-1;i>=0;i--) cout<<consensus_a[i];
- cout<<endl;
- for(int j=tick-1;j>=0;j--) cout<<consensus_b[j];
- cout<<endl;*/
-
- free(H_cur_row);
- free(H_prev_row);
- free(Last_row);
- free(Last_col);
- return 1;
-} // END of main
-
-
-
-
-/////////////////////////////////////////////////////////////////////////////
-// auxiliary functions used by main:
-/////////////////////////////////////////////////////////////////////////////
-
-
-/*void checkfile(int open, char filename[]){
-
- if (open){cout << "Error: Can't open the file "<<filename<<endl;exit(1);}
- else cout<<"Opened file "<<filename<<endl;
-}*/
-
-/////////////////////////////////////////////////////////////////////////////
-
-double similarity_score(char a,char b){
-
- double result;
- if(a==b){
- result=1.;
- }
- else{
- result=-mu;
- }
- return result;
-}
-
-/////////////////////////////////////////////////////////////////////////////
-
-double find_array_max(double array[],int length){
-
- double max = array[0]; // start with max = first element
-
- for(int i = 1; i<length; i++){
- if(array[i] > max){
- max = array[i];
- }
- }
- return max; // return highest value in array
-}
-
-/////////////////////////////////////////////////////////////////////////////
-/*
-string read_sequence(ifstream& f)
-{
- // overflows.
- string seq;
- char line[5000];
- while( f.good() )
- {
- f.getline(line,5000);
- // cout << "Line:" << line << endl;
- if( line[0] == 0 || line[0]=='#' )
- continue;
- for(int i = 0; line[i] != 0; ++i)
- {
- int c = toupper(line[i]);
- if( c != 'A' && c != 'G' && c != 'C' && c != 'T' )
- continue;
- //cout << char(c);
- seq.push_back(char(c));
- }
- }
- return seq;
-}*/
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/output_contigs.py b/external/gatb-minia-pipeline/BESST/BESST/diploid/output_contigs.py
deleted file mode 100644
index 3f050902d5a24353096552f47ff11f51f084304c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid/output_contigs.py
+++ /dev/null
@@ -1,229 +0,0 @@
-'''
-Created on Jun 19, 2013
-
-@author: ksahlin
-'''
-
-import os
-
-import networkx as nx
-
-from BESST import Contig, Scaffold
-import smith_waterman
-
-def reverse_complement(string):
- #rev_nuc = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'N':'N', 'X':'X'}
- # Modified for Abyss output
- rev_nuc = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'a':'t', 'c':'g', 'g':'c', 't':'a', 'N':'N', 'X':'X', 'n':'n', 'Y':'R', 'R':'Y', 'K':'M', 'M':'K', 'S':'S', 'W':'W', 'B':'V', 'V':'B', 'H':'D', 'D':'H', 'y':'r', 'r':'y', 'k':'m', 'm':'k', 's':'s', 'w':'w', 'b':'v', 'v':'b', 'h':'d', 'd':'h'}
-
- rev_comp = ''.join([rev_nuc[nucl] for nucl in reversed(string)])
- return(rev_comp)
-
-def k_mer_graph_to_scaffold_graph(graph, removed):
- ''' We want to make new contigs of the haplotypic regions that we have solved.
- The regions that we have solved are the ones where a node has precisely
- one neighbor in the overlapping k-mer graph.
-
- '''
-
- new_contigs = nx.Graph()
-
- for edge in graph.edges_iter():
- try:
- graph.edge[edge[0]][edge[1]]['m']
- node = edge[0]
- nbr = edge[1]
- except KeyError:
- continue
- ##
- # Modulo 2 operator to see what contig end we should map to
- # Beginning and forward of contig, or end and reverse compl. -> "Left" side of contig
- # Othervise right side
-
- if node[1] == 0:
- new_node1 = (node[0], 'L')
- other_side1 = (node[0], 'R')
- else:
- new_node1 = (node[0], 'R')
- other_side1 = (node[0], 'L')
-
- if nbr[1] == 0:
- new_node2 = (nbr[0], 'L')
- other_side2 = (nbr[0], 'R')
- else:
- new_node2 = (nbr[0], 'R')
- other_side2 = (nbr[0], 'L')
- new_contigs.add_edge(new_node1, new_node2)
- new_contigs.add_edge(new_node1 , other_side1)
- new_contigs.add_edge(new_node2 , other_side2)
-
- new_removed = {}
- for rem, used in removed.items():
- #if rem[1] == used[1] :
- new_removed[(rem[0], 'L')] = (used[0], 'L')
- new_removed[(rem[0], 'R')] = (used[0], 'R')
- #else:
- # new_removed[(rem[0], 'L')] = (used[0], 'R')
- # new_removed[(rem[0], 'R')] = (used[0], 'L')
-
- print len(new_contigs.nodes())
- return(new_contigs, new_removed)
-
-def get_joined_sequence(contigs, sub_graph, start, end, k_mer_size, removed):
- sequence = ''
- print 'Nr nodes subgraph:', len(sub_graph.nodes())
- path = nx.algorithms.shortest_path(sub_graph, start, end)
- path_len = len(path)
- print 'Nr contigs in path:', path_len / 2.0
-
- index_to_remove = []
- for i, node in enumerate(path):
- if i % 2 == 0:
- try:
- contigs[node[0]]
- except KeyError:
- print 'Contig already removed. Number ' + str(i) + ' in path of length' + str(len(path))
- if i == 0 or i == len(path) - 2:# end contig. Just regular haplotype!
- print 'End contig. Just regular haplotype! continue merging'
- index_to_remove.append(i)
- index_to_remove.append(i + 1)
- else:
- print 'It is contig:', node[0]
- return()
- for index in sorted(index_to_remove, reverse=True):
- #path[index] = removed[path[index]]
- print 'Trouble with dissappeared haplotype here!'
- print path[index], removed[path[index]]
- del path[index]
-
- path_len = len(path)
- for i, node in enumerate(path):
- if i % 2 == 1 and i < path_len - 2:
- ctg1 = contigs[node[0]] if node[1] == 'R' else reverse_complement(contigs[node[0]])
- seq1 = ctg1[:k_mer_size - 1]
- if i == 1:
- sequence += ctg1
-
- ctg2 = contigs[path[i + 1][0]] if path[i + 1][1] == 'L' else reverse_complement(contigs[path[i + 1][0]])
- seq2 = ctg2[:k_mer_size - 1]
- score, max_i, max_j = smith_waterman.SW(seq1, seq2, 0, 0)
- neg_gap = min(max_i, max_j)
- sequence += ctg2[neg_gap:]
- # Remove the contigs that are included in a new contig so
- # that we don't print it out several times
- del contigs[node[0]]
-
- return(sequence)
-
-def merge_ctgs(new_contigs, removed, node):
- replacing_hapl = removed[node]
- other_side_hapl = (replacing_hapl[0], 'R') if replacing_hapl[1] == 'L' else (replacing_hapl[0], 'L')
- if len(new_contigs.neighbors(other_side_hapl)) > 1:
- print "warning!: Trying to merge haploid that are not ends of components"
- print other_side_hapl, new_contigs.neighbors(other_side_hapl)
- return()
- other_side = (node[0], 'R') if node[1] == 'L' else (node[0], 'L')
- nbrs = new_contigs.neighbors(other_side)
- nbr = filter(lambda x: x[0] != other_side[0], nbrs)
- if len(nbr) > 1:
- print "Warning: many neighbors for haplotype "
- nbr = nbr[0]
- new_contigs.remove_node((node[0], 'R'))
- new_contigs.remove_node((node[0], 'L'))
- new_contigs.add_edge(nbr, other_side_hapl)
- return()
-
-def get_remaining_overlaps(new_contigs, removed):
-
- for component in nx.connected_component_subgraphs(new_contigs):
- for node in component:
- if len(new_contigs.neighbors(node)) == 1:
- start = node
- break
- for node in component:
- if len(new_contigs.neighbors(node)) == 1 and node != start:
- end = node
- break
- if start in removed:
- merge_ctgs(new_contigs, removed, start)
- if end in removed:
- merge_ctgs(new_contigs, removed, end)
-
- return()
-
-
-def print_out_contigs(contigs, new_contigs, output_dir, k_mer_size, removed):
- contigs_out = open(os.path.join(output_dir, 'BESST_contigs.fa'), 'w')
-
- contig_index = 0
- for comp in nx.connected_component_subgraphs(new_contigs):
- print len(comp.nodes()) / 2.0
-
- get_remaining_overlaps(new_contigs, removed)
-
- print 'After merge:'
- for comp in nx.connected_component_subgraphs(new_contigs):
- print len(comp.nodes()) / 2.0
-
- for component in nx.connected_component_subgraphs(new_contigs):
- contig_index += 1
- accession = '>BESST_ctg' + str(contig_index)
-
- for node in component:
- if len(new_contigs.neighbors(node)) == 1:
- start = node
- break
- for node in component:
- if len(new_contigs.neighbors(node)) == 1 and node != start:
- end = node
- break
- ctg_seq = get_joined_sequence(contigs, component, start, end, k_mer_size, removed)
- if ctg_seq:
- print >> contigs_out, accession + '\n' + ctg_seq
-
-
-
-
- # Print out remaining contigs (the ones that has not been
- # removed as haplotypes or merged into bigger contigs)
- print len(contigs)
- cntru = 0
- for acc, sequence in contigs.items():
- cntru += 1
- print >> contigs_out, '>' + acc + '\n' + sequence
- print cntru, ' contigs that were kept as they are (not merged or removed).'
- return()
-
-def generate_fasta(graph, contigs, output_dir, k_mer_size):
-
- haplotypes = open(os.path.join(output_dir, 'haplotypes.fa'), 'w')
- nodes_to_remove = set()
- haplotype_count = 0
- removed = {}
- for node in graph:
- if graph.node[node]['r']:
- nodes_to_remove.add(node)
- nbrs = graph.neighbors(node)
- for nbr in nbrs:
- if graph.edge[node][nbr].keys() == ['a']:
- #print node
- #print 'nbr!!:', nbr
- removed[node] = nbr
-
- graph.remove_nodes_from(nodes_to_remove)
- for node in nodes_to_remove:
- # remove the nodes from the contig dictionary as well
- # so that we do not print them out among the new contigs.
- try:
- print >> haplotypes, '>' + node[0].strip() + '\n' + contigs[node[0]]
- del contigs[node[0]]
- haplotype_count += 1
- except KeyError:
- pass
-
- print 'Number of haplotypes removed:', haplotype_count
- print 'Nr allele nodes removed:', len(removed)
- new_contigs, removed = k_mer_graph_to_scaffold_graph(graph, removed)
- print_out_contigs(contigs, new_contigs, output_dir, k_mer_size, removed)
-
- return()
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/remap_to_contigs.py b/external/gatb-minia-pipeline/BESST/BESST/diploid/remap_to_contigs.py
deleted file mode 100644
index eb6b5f8e31f234ee2ed9d2dffb27efb15c39607b..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid/remap_to_contigs.py
+++ /dev/null
@@ -1,5 +0,0 @@
-'''
-Created on Jun 18, 2013
-
-@author: ksahlin
-'''
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/smith_waterman.py b/external/gatb-minia-pipeline/BESST/BESST/diploid/smith_waterman.py
deleted file mode 100644
index 69159d398717f29e4196d8be9d6f80809580bbba..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid/smith_waterman.py
+++ /dev/null
@@ -1,107 +0,0 @@
-'''
-Created on Jun 17, 2013
-
-@author: ksahlin
-'''
-
-
-
-def traceback_parser(score, row, column, traceback_matrix, seq1, seq2):
-
- s_i = []
- s_j = []
-
- stepcounter = 0
- while True:
- stepcounter += 1
- if traceback_matrix[row][column] == 1:
- s_i.append(seq1[row - 1])
- s_j.append(seq2[column - 1])
- row = row - 1
- column = column - 1
- elif traceback_matrix[row][column] == 3:
- s_i.append('-')
- s_j.append(seq2[column - 1])
- column = column - 1
- elif traceback_matrix[row][column] == 2:
- s_i.append(seq1[row - 1])
- s_j.append('-')
- row = row - 1
- else:
- break
-
- s_i.reverse()
- s_j.reverse()
-
- return -(stepcounter - 1) # s_i,s_j
-
-def score(a, b, match_score, mismatch_penalty):
- if a == b:
- s = match_score
- if a != b:
- s = mismatch_penalty
-
- return s
-
-def zero_maker(n, m):
- res_row = []
- res_all = []
-
- for i in range(n):
- temp = []
- for j in range(m):
- temp.append(0)
- res_all.append(temp)
- del(temp)
- return res_all
-
-def SW(seq1, seq2, gap_penalty, mismatch_penalty):
- score_matrix = zero_maker(len(seq1) + 1, len(seq2) + 1)
- traceback_matrix = zero_maker(len(seq1) + 1, len(seq2) + 1)
-
- for i in range(1, len(seq1) + 1):
- for j in range(1, len(seq2) + 1):
- substitution_score = score_matrix[i - 1][j - 1] + score(seq1[i - 1], seq2[j - 1], 1, mismatch_penalty)
- i_indel = score_matrix[i - 1][j] + gap_penalty
- j_indel = score_matrix[i][j - 1] + gap_penalty
- score_matrix[i][j] = max(substitution_score, i_indel, j_indel)
-
- if score_matrix[i][j] == substitution_score:
- traceback_matrix[i][j] = 1
- elif score_matrix[i][j] == i_indel:
- traceback_matrix[i][j] = 2
- elif score_matrix[i][j] == j_indel:
- traceback_matrix[i][j] = 3
-
- n = len(score_matrix) #nr of rows
- m = len(score_matrix[0]) #nr or columns
- max_score = 0
-
- #if in last column
- for i in range(0, n):
- if score_matrix[i][m - 1] >= max_score:
- max_i = i
- max_j = m - 1
- max_score = score_matrix[i][m - 1]
-
- #if in last row
- for j in range(0, m):
- if score_matrix[n - 1][j] >= max_score:
- max_i = n - 1
- max_j = j
- max_score = score_matrix[n - 1][j]
-
-
- #Returnera score har
-
- return max_score, max_i, max_j
-
-
-if __name__ == '__main__':
- seq1 = 'TTAGCCACTG' * 20
- seq2 = 'TTTGCTGGAG' * 20
- score, row, column, traceback_matrix = SW(seq1, seq2, -1, -3)
- b = traceback_parser(score, row, column, traceback_matrix, seq1, seq2)
- print b
- #print score_matrix
-#print traceback_matrix
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid/wrapper_sw.py b/external/gatb-minia-pipeline/BESST/BESST/diploid/wrapper_sw.py
deleted file mode 100644
index f4e1c6c954ba4daa197e8f907aff59cde65aa63c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid/wrapper_sw.py
+++ /dev/null
@@ -1,28 +0,0 @@
-'''
-Created on Jun 26, 2013
-
-@author: ksahlin
-'''
-
-import ctypes
-import os
-
-import BESST.diploid
-
-class ReturnValues(ctypes.Structure):
- _fields_ = [("score", ctypes.c_int),
- ("i_max", ctypes.c_int),
- ("j_max", ctypes.c_int)]
-
-def wrap_sw(seq1, seq2, mu, delta):
- c_s1 = ctypes.c_char_p(seq1)
- c_s2 = ctypes.c_char_p(seq2)
- res = ReturnValues(0, 0, 0)
- path = os.path.join( '/'.join(BESST.diploid.__file__.split('/')[:-1] ), 'lib/smith_waterman.so' )
- SW_fcn = ctypes.CDLL(path) #BESST/diploid/
- SW_fcn.SW(c_s1, c_s2, ctypes.byref(res)) # linux or when mingw used on windows
- return(res.score, res.i_max, res.j_max)
-
-if __name__ == '__main__':
- wrap_sw('AGAAGGAAGGGGGAGAGTTTG',
- 'AGAAGGAAGGTTGGGAGAGTTTG' , 0, 0)
diff --git a/external/gatb-minia-pipeline/BESST/BESST/diploid_main.py b/external/gatb-minia-pipeline/BESST/BESST/diploid_main.py
deleted file mode 100644
index 040609bdb682a3741357e065741c383c4f4adcd3..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/diploid_main.py
+++ /dev/null
@@ -1,15 +0,0 @@
-'''
-Created on Jun 17, 2013
-
-@author: ksahlin
-'''
-
-import diploid
-
-def main(contigs):
- kmer_dict, contig_dict = diploid.get_kmers(contigs)
- potential_haplotypes = diploid.get_haplotype_regions(kmer_dict, contig_dict)
- diploid.smith_waterman(potential_haplotypes)
-
- return
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/errorhandle.py b/external/gatb-minia-pipeline/BESST/BESST/errorhandle.py
deleted file mode 100644
index 6f0738928e87745e442bafc439225d642e78083c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/errorhandle.py
+++ /dev/null
@@ -1,101 +0,0 @@
-'''
-Created on Aug 4, 2013
-
-@author: ksahlin
-'''
-
-import sys
-#from argparse import ArgumentError
-
-
-def module_exists(module_name):
- try:
- __import__(module_name)
- except ImportError:
- return False
- else:
- return True
-
-
-
-##
-# Error handling for modules
-
-def check_module(module):
- if not module_exists(module):
- sys.stdout.write('Uninstalled module: ' + module + '\n')
- sys.stdout.write('Please install ' + module + ' using one of the two provided commands from terminal:\n \
- pip install ' + module + '\n \
- easy_install ' + module + '\n')
- sys.exit(1)
-
-
-
-def parse_check(arg, parser):
-
- ##
- # Error handling for files
-
- for file_ in arg.bamfiles:
- try:
- open(file_)
- except IOError as e:
- sys.exit("couldn't find BAM file: " + file_ + " check that the path is correct and that the file exists")
- try:
- open(file_ + '.bai')
- except IOError as e:
- print "couldn't find index file: ", file_ + '.bai', " check that the path is correct and that the file exists"
- sys.exit(0)
-
- try:
- open(arg.contigfile)
- except IOError as e:
- sys.exit("couldn't open contig file " + arg.contigfile + " check that the path is correct and that the file exists")
-
-
- ##
- # Error handling when parsing arguments
- if arg.orientation == None:
- sys.stdout.write('Warning: Orientations of library mappings not specified. Treating all libraries as fr mapped.\
- If this is not the case, please provide orientations with the --orientations parameter.\n')
- sys.stderr.write('Warning: Orientations of library mappings not specified. Treating all libraries as fr mapped.\
- If this is not the case, please provide orientations with the --orientation parameter.\n')
- elif arg.orientation != None and not len(arg.orientation) == len(arg.bamfiles):
- sys.exit("Number of arguments doesn't match between -f and --orientation. Give one orientation for each library.\n")
-
- elif not all([x == 'fr' or x == 'rf' for x in arg.orientation]):
- sys.exit("'rf' and 'fr' are the only valid strings to --orinentation.\n")
-
-
- if not all([x == None or len(x) == len(arg.bamfiles) for x in [arg.stddev , arg.mean , arg.readlen, arg.edgesupport, arg.covcutoff, arg.threshold, arg.minsize]]):
- parser.error("If any of the below following options are specified, they should have the same number of arguments as the number of BAM files.\n {0}, {1}, {2}, {3}, {4}, {5}, {6}, {7} ".format("bamfiles", "mean", "stddev", "readlen", "edgesupport",
- "covcutoff", "threshold", "minsize"))
-
- if (arg.mean and not arg.stddev) or (not arg.mean and arg.stddev):
- parser.error("either both or none of -m and -s is required")
- if (arg.threshold and not arg.minsize) or (not arg.threshold and arg.minsize):
- parser.error("either both or none of -T and -k is required")
- if not arg.contigfile:
- parser.error("parameter -c (a fasta contig file) is required")
- if not arg.bamfiles:
- parser.error("parameter -f (BAM files) is required")
-
- if arg.multiprocess:
- sys.stdout.write('Warning: -q specified but will not be activated. The multiprocess option was found to contain a bug\
- and will therefore not be activated.\n')
- arg.multiprocess = False
-
- if arg.haplotype:
- sys.stdout.write('Warning: -g (haplotype aware scaffolding) specified but this option is under construction and not stable. \
- This option will therefore be inactivated. \n')
- arg.haplotype = False
-
- return()
-
-##
-# Throw warning if contig present in bam file but not seen in contig fasta file.
-# This can happen if fasta file is filtered after alignment
-
-def unknown_contig(ctg):
- sys.stdout.write('Contig: ' + ctg + ' was seen in BAM file but is not present in contig fasta file.\
- If this is expected (i.e. due to filtering after alignment), please ignore.\n')
diff --git a/external/gatb-minia-pipeline/BESST/BESST/find_bimodality.py b/external/gatb-minia-pipeline/BESST/BESST/find_bimodality.py
deleted file mode 100644
index ee3cbe70c37fd3e486aa297ed81723670ea10ff3..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/find_bimodality.py
+++ /dev/null
@@ -1,205 +0,0 @@
-'''
-Created on Sep 29, 2011
-
-@author: ksahlin
-
-This file is part of BESST.
-
-BESST is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-BESST is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with BESST. If not, see <http://www.gnu.org/licenses/>.
-'''
-import sys
-
-import numpy as np
-import math
-
-
-
-def params(x):
- n = float(len(x))
- mu = sum(x)/ float(len(x))
- x_sq = sum(map(lambda x: x ** 2, x))
- var = (x_sq - n * mu ** 2) / (n - 1)
- return mu, var
-
-
-def checkEqualIvo(lst):
- return not lst or lst.count(lst[0]) == len(lst)
-
-def split_distribution(all_isizes):
- """ Split a population into sub-populations
-
- Based on binning the data into n_bins and finding contigous groups of non-empty bins.
-
- Returns [lowest, ..., highest] all of which are sorted sequences
-
- EXAMPLE:
- all_isizes = [2, 1, 2, 1, 2, 3, 3, 3, 2, 1, 2,
- 3, 4, 5, 6, 6, 7, 8, 9, 10, 11, 11,
- 12, 12, 11, 13, 11, 12, 13, 11, 12,
- 13, 1, 2, 3, 2, 1, 3]
-
- find_bimodality.split_population2(all_isizes,20)
-
- bins = [ 1. 1.6 2.2 2.8 3.4 4. 4.6 5.2 5.8 6.4 7. 7.6
- 8.2 8.8 9.4 10. 10.6 11.2 11.8 12.4 13. ]
-
- # n bins (set by n_bins parameter) will always create n+2 sublists as seen below
- binned = [[], [1, 1, 1, 1, 1], [2, 2, 2, 2, 2, 2, 2], [], [3, 3, 3, 3, 3, 3],
- [], [4], [5], [], [6, 6], [], [7], [8], [], [9], [], [10],
- [11, 11, 11, 11, 11], [], [12, 12, 12, 12], [], [13, 13, 13]]
-
- # we join them to clusters
- joined_bins = [[1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2], [3, 3, 3, 3, 3, 3],
- [4, 5], [6, 6], [7, 8], [9], [10, 11, 11, 11, 11, 11],
- [12, 12, 12, 12], [13, 13, 13]]
-
- # joined_bins contains 9 sublists. Now we split joined_bins into two sublists
- # by splitting joined_bins at each position 1,...,8. The variance of the two sublists
- # are thereafter calculated and summed up. We return the two sublists (i.e., clusters/populations)
- # that gives the lowest sum. For this example we return:
-
- cluster1 = [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 5, 6, 6, 7, 8]
- cluster2 = [9, 10, 11, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13, 13]
- mean1 = 3.0416666666666665
- stddev1 = 1.9886453039512946
- mean2 = 11.5
- stddev2 = 1.1602387022306428
-
- Values will slightly change with value on n_bins. It is recommended to choose n_bins
- too high rather than too low. For isize data, choose e.g., n_bins = max_isize
-
- ###########################################################################
- Some other tests
-
- We don't want to split l5 (approx normal dist) and l2,l4 since theu have one mode and fat tailed.
- l1 and l3 have two modes.
- >>> l
- [2, 1, 2, 1, 2, 3, 3, 3, 2, 1, 2, 3, 4, 5, 6, 6, 7, 8, 9, 10, 11, 11, 12, 12, 11, 13, 11, 12, 13, 11, 12, 13, 1, 2, 3, 2, 1, 3]
- >>> l2
- [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 9, 9, 10, 10, 11]
- >>> l3
- [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 7, 7, 7, 8, 8, 9, 9, 10, 10, 11]
- >>> l4
- [1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 8, 8, 9, 10, 11]
- >>> l5
- [1, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 7, 7, 7, 8, 8, 9]
- >>> find_bimodality.split_distribution(l)
- ([1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 5, 6, 6, 7], [8, 9, 10, 11, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13, 13], 2.8260869565217392, 1.7228985595908761, 11.266666666666667, 1.4375905768565118)
- >>> find_bimodality.split_distribution(l2)
- ([1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 9, 9, 10, 10, 11], [], 4.621621621621622, 2.8901302484235636, 0, 0)
- >>> find_bimodality.split_distribution(l3)
- ([1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3], [7, 7, 7, 8, 8, 9, 9, 10, 10, 11], 2.1176470588235294, 0.781213234429025, 8.6, 1.4298407059684846)
- >>> find_bimodality.split_distribution(l4)
- ([1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 8, 8, 9, 10, 11], [], 4.264705882352941, 2.711466376496939, 0, 0)
- >>> find_bimodality.split_distribution(l5)
- ([1, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 7, 7, 7, 8, 8, 9], [], 5.0, 1.8754309849499513, 0, 0)
- """
-
- sorted_isizes = sorted(all_isizes)
- n_bins = sorted_isizes[-1]*2
- # bin the data into n_bins in a 2d structure, one sequence for each bin:
- _ , bins = np.histogram(sorted_isizes, bins=n_bins)
- # print bins
- bin_indices = np.digitize(sorted_isizes, bins)
- # print bin_indices
- binned = []
- for i in range(len(bins)+1):
- binned.append([])
- for ix_bin, v in zip(bin_indices, sorted_isizes):
- binned[ix_bin].append(v)
- # print binned
-
- # now join-up non-empty bins
- joined_bins = [[]] # so 2D, with initially 1 sub-list
- len_last_bin = 0
- for bin in binned:
- len_bin = len(bin)
- if len_bin == 0 and len_last_bin != 0: # will correctly handle the case where bin 0 is empty
- joined_bins.append([])
- if len_bin != 0:
- joined_bins[-1].extend(bin)
- len_last_bin = len_bin
-
-
- # special case: only one bin was detected, probably due to a tight cluster
- # i.e. no split distributions
- if len(joined_bins) < 2:
- observations = [item for sublist in joined_bins for item in sublist]
- mu, var = params(observations)
- stddev = math.sqrt(var)
- mean = mu
- return cluster1, [], mean1, stddev1, 0, 0
-
-
-
- # if we are here we passed the special case of only one cluster
- # we calculate the mean and stddev for the base case now.
- # the base case is that there is in fact only one cluster of isizes
- # and there is no need to separete observations. We will later on compare this
- # base case varaince to variances when splitting the distribution.
-
- observations = [item for sublist in joined_bins for item in sublist]
- filter_observations = filter(lambda x: x>100, observations)
- if len(filter_observations) < 2:
- return [],[],0,0,0,0
- base_mu, base_var = params(filter_observations)
- base_stddev = math.sqrt(base_var)
- mean = base_mu
- # print "base", base_mu, base_stddev, base_var
-
- #calculate sum of two varinaces from the two sublists when splitting
- # this list of list into two. We ar guaranteed to calculate the varance for
- # at most n+1 pairs of lists. In practice often fewer times.
- # print 'JOINED BINS:', joined_bins
-
-
- # initialze lowest var to the variance given that there is only one cluster of isizes
- lowest_var = base_var
- lowest_stddev = base_stddev
- # print lowest_var, lowest_stddev
- split_index = 0
-
- for i in range(1,len(joined_bins)):
- observations1 = [item for sublist in joined_bins[:i] for item in sublist]
- observations2 = [item for sublist in joined_bins[i:] for item in sublist]
- # print observations1
- # print observations2
- if len(observations1) < 2 or len(observations2) < 2 or checkEqualIvo(observations1) or checkEqualIvo(observations2):
- continue
- mu1, var1 = params(observations1)
- mu2, var2 = params(observations2)
- # print 'mu1', mu1
- # print 'mu2', mu2
-
- sum_var = var1 + var2
- sum_stddev = math.sqrt(var1) + math.sqrt(var2)
- # print sum_var, sum_stddev
- if sum_var < lowest_var and sum_stddev < lowest_stddev:
- lowest_var = sum_var
- lowest_stddev = sum_stddev
- stddev1 = math.sqrt(var1)
- stddev2 = math.sqrt(var2)
- mean1 = mu1
- mean2 = mu2
- split_index = i
-
- if lowest_var < base_var and lowest_stddev < base_stddev:
- cluster1 = [item for sublist in joined_bins[:split_index] for item in sublist]
- cluster2 = [item for sublist in joined_bins[split_index:] for item in sublist]
- return cluster1, cluster2, mean1, stddev1, mean2, stddev2
-
- else:
- cluster1 = [item for sublist in joined_bins for item in sublist]
- base_stddev = math.sqrt(base_var)
- return cluster1, [], base_mu, base_stddev, 0, 0
diff --git a/external/gatb-minia-pipeline/BESST/BESST/haplotypes.py b/external/gatb-minia-pipeline/BESST/BESST/haplotypes.py
deleted file mode 100644
index c941dffeaf4ec27c417ac3db95491b7e23577467..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/haplotypes.py
+++ /dev/null
@@ -1,124 +0,0 @@
-'''
-Created on Mar 11, 2013
-
-@author: ksahlin
-'''
-
-
-import networkx as nx
-
-
-def HaplotypicRegions(G, G_prime, Contigs, Scaffolds, param, Information):
- CB = nx.cycle_basis(G)
- cb_6 = 0
- cb_6_true = 0
- cb_else_true = 0
- potentially_merged = 0
- tot_nr_contigs_merged = 0
- strange_cases = 0
-
- for cycle in CB:
- str_case_abort = False
- contigs = [node[0] for node in cycle]
- d = {}
-
-####### Very temporary implementation of dealing with haplotypes!!! #########
- if len(cycle) >= 6:
- for i in contigs: d[i] = d.has_key(i)
- singles = [k for k in d.keys() if not d[k]]
- if len(singles) == 2:
- cb_else_true += 1
- #find length of the two paths between the source and sink
- haplotype_region = True
- #first path
- #get sink and source
- try:
- cycle.index((singles[0], 'L'))
- source_node = (singles[0], 'L')
- except ValueError:
- source_node = (singles[0], 'R')
- try:
- cycle.index((singles[1], 'L'))
- sink_node = (singles[1], 'L')
- except ValueError:
- sink_node = (singles[1], 'R')
-
- #check if region has been removed in some previuos step: this suggests some strange region
- for scaf in cycle:
- if not scaf[0] in Scaffolds:
- strange_cases += 1
- #print 'STRANGE!'
- str_case_abort = True
- if str_case_abort:
- continue
-
- sub_G = nx.subgraph(G, cycle)
- path = nx.algorithms.shortest_path(sub_G, source=source_node, target=sink_node)
-
-
- ## Get length of path (OBS: gaps not implemented yet!!) ##
- #print 'First path' ,path
- length_path1 = 0
- nr_contigs_path1 = 0
- for scaffold_ in path:
- scaffold = scaffold_[0]
- if sink_node != scaffold_ and source_node != scaffold_:
- length_path1 += Scaffolds[scaffold].s_length
- nr_contigs = len(Scaffolds[scaffold].contigs)
- #if nr_contigs > 1:
- # print 'More than one contig in scaffold, contigs are:'
- for cont_obj in Scaffolds[scaffold].contigs:
- nr_contigs_path1 += 1
- #print 'Haplotype: ', cont_obj.is_haplotype, cont_obj.coverage
- if not cont_obj.is_haplotype:
- # print 'Not haplotype'
- haplotype_region = False
-
-
-
- #print 'Total length of path 1: ', length_path1/2.0
-
- set_of_nodes = set(path)
- start_end = set([source_node, sink_node])
- tot_set = set(cycle)
- nodes_to_remove = set_of_nodes.symmetric_difference(start_end)
- remaining_path = tot_set.symmetric_difference(nodes_to_remove)
- #print 'Secont path', remaining_path
- length_path2 = 0
- nr_contigs_path2 = 0
- for scaffold_ in remaining_path:
- scaffold = scaffold_[0]
- if sink_node != scaffold_ and source_node != scaffold_:
- length_path2 += Scaffolds[scaffold].s_length
- nr_contigs = len(Scaffolds[scaffold].contigs)
- #if nr_contigs > 1:
- # print 'More than one contig in scaffold'
- for cont_obj in Scaffolds[scaffold].contigs:
- nr_contigs_path2 += 1
- #print 'Haplotype: ', cont_obj.is_haplotype, cont_obj.coverage
- if not cont_obj.is_haplotype:
- haplotype_region = False
-
- try:
- if length_path2 / float(length_path1) < param.hapl_ratio or length_path1 / float(length_path2) > 1 / param.hapl_ratio and haplotype_region:
- potentially_merged += 1
- tot_nr_contigs_merged += nr_contigs_path2 / 2.0
- #Remove all contigs from path 2
- to_remove = remaining_path.symmetric_difference(start_end)
- G.remove_nodes_from(to_remove)
- G_prime.remove_nodes_from(to_remove)
- for node in to_remove:
- try: #remove scaffold with all contigs
- for contig_obj in Scaffolds[node[0]].contigs:
- del Contigs[contig_obj.name]
- del Scaffolds[node[0]]
- except KeyError: #scaffold and all contigs has already been removed since to_revove-path contains two nodes for each scaffold
- pass
- except ZeroDivisionError:
- pass
-
- print >> Information, 'NR of other interesting cycles: ', cb_else_true
- print >> Information, 'Potential hapl regions treated: ', potentially_merged
- print >> Information, 'Potential hapl contigs "removed": ', tot_nr_contigs_merged
- print >> Information, 'Nr of strange cases (contigs occurring in multiple regions): ', strange_cases
- return()
diff --git a/external/gatb-minia-pipeline/BESST/BESST/libmetrics.py b/external/gatb-minia-pipeline/BESST/BESST/libmetrics.py
deleted file mode 100644
index 1051c4ac8bbf21a63ef88187d33695e54299f1b5..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/libmetrics.py
+++ /dev/null
@@ -1,426 +0,0 @@
-'''
-Created on Mar 7, 2013
-
-@author: ksahlin
-'''
-
-import sys
-import math
-
-from heapq import nlargest
-
-from mathstats.normaldist.normal import MaxObsDistr
-from BESST import bam_parser
-from BESST import find_bimodality
-from BESST import plots
-
-def AdjustInsertsizeDist(mean_insert, std_dev_insert, insert_list):
- k = MaxObsDistr(len(insert_list), 0.95)
- filtered_list = list(filter((lambda x : (x < mean_insert + k * std_dev_insert and x > mean_insert - k * std_dev_insert)), insert_list))
- if len(insert_list) > len(filtered_list):
- return(True, filtered_list)
- else:
- return(False, filtered_list)
-
-def remove_outliers(ins_size_reads):
- ## SMOOTH OUT THE MEAN HERE by removing extreme observations
- if not ins_size_reads:
- return 0,0
- n = float(len(ins_size_reads))
- mean_isize = sum(ins_size_reads) / n
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), ins_size_reads))) / (n - 1)) ** 0.5
- extreme_obs_occur = True
- while extreme_obs_occur:
- extreme_obs_occur, filtered_list = AdjustInsertsizeDist(mean_isize, std_dev_isize, ins_size_reads)
- n = float(len(filtered_list))
- mean_isize = sum(filtered_list) / n
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), filtered_list))) / (n - 1)) ** 0.5
- ins_size_reads = filtered_list
- n = float(len(ins_size_reads))
- mean_isize = sum(ins_size_reads) / n
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), ins_size_reads))) / (n - 1)) ** 0.5
- return mean_isize, std_dev_isize
-
-def get_contamination_metrics(largest_contigs_indexes, bam_file, cont_names, param, Information):
- iter_threshold = 1000000
- counter_total= 0
- count_contamine = 0
-
- contamination_reads = []
- sample_counter = 0
-
- # for index in largest_contigs_indexes:
- # try:
- # iter_ = bam_file.fetch(cont_names[index])
- # except ValueError:
- # sys.stderr.write('Need indexed bamfiles, index file should be located in the same directory as the BAM file\nterminating..\n')
- # sys.exit(0)
- for read in bam_file:
- # all reads mapping
- if read.rname in largest_contigs_indexes:
- sample_counter += 1
- if not read.is_unmapped: ##read.tid == read.rnext and not read.mate_is_unmapped and not read.is_unmapped: #
- counter_total += 1
-
- # contamination reads (mapped in reverse complemented orientation)
- if param.orientation == 'fr' and bam_parser.is_proper_aligned_unique_outie(read):
- frag_size = abs(read.tlen)+2*param.read_len
- if param.read_len < frag_size:
- contamination_reads.append(frag_size)
- count_contamine += 2
-
- if param.orientation == 'rf' and bam_parser.is_proper_aligned_unique_innie(read):
- frag_size = abs(read.tlen)
- if param.read_len < frag_size:
- contamination_reads.append(frag_size)
- count_contamine += 2
-
- if sample_counter >= iter_threshold:
- break
-
- ## SMOOTH OUT contamine distribution here by removing extreme observations##
-
- n_contamine = float(len(contamination_reads))
- mean_isize = 0
- std_dev_isize = 0
- if n_contamine > 2:
- mean_isize = sum(contamination_reads) / n_contamine
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), contamination_reads))) / (n_contamine - 1)) ** 0.5
- print >> Information, 'Contamine mean before filtering :', mean_isize
- print >> Information, 'Contamine stddev before filtering: ', std_dev_isize
- # #new method to find distribution
- # dist1, dist2, mean_isize, std_dev_isize, outliers_mean, outliers_stddev = find_bimodality.split_distribution(contamination_reads)
- # n_contamine = len(dist1)
- extreme_obs_occur = True
- while extreme_obs_occur:
- extreme_obs_occur, filtered_list = AdjustInsertsizeDist(mean_isize, std_dev_isize, contamination_reads)
- n_contamine = float(len(filtered_list))
- if n_contamine > 2:
- mean_isize = sum(filtered_list) / n_contamine
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), filtered_list))) / (n_contamine - 1)) ** 0.5
- contamination_reads = filtered_list
- else:
- break
- print >> Information, 'Contamine mean converged:', mean_isize
- print >> Information, 'Contamine std_est converged: ', std_dev_isize
-
- contamination_ratio = 2*n_contamine / float(counter_total)
-
- if mean_isize >= param.mean_ins_size or std_dev_isize >= param.std_dev_ins_size or contamination_ratio <= 0.05:
- # either contamine mean or stddev is higher than MP lb mean which means it's spurious alignments or
- # other wierd thing -> no true PE-contamine as artifact discribed in the illumina MP construction protocol.
- # or we have less than 5% of contamine reads. Then we skip dealing with them since they constitute such a small
- # fraction of the total reads and introduce more complexity when orienting scaffolds in pathfinder module
- param.contamination_ratio = False
- param.contamination_mean = 0
- param.contamination_stddev = 0
- else:
- param.contamination_mean = mean_isize
- param.contamination_stddev = std_dev_isize
- param.contamination_ratio = contamination_ratio
-
- bam_file.reset()
- return n_contamine
-
-def argmax(iterable):
- return max(enumerate(iterable), key=lambda x: x[1])[0]
-
-def sum_chunks(l, n):
- """Yield successive n-sized chunks from l."""
- for i in xrange(0, len(l), n):
- yield sum(l[i:i+n])
-
-def getdistr(ins_size_reads, cont_lengths_list, param, Information):
- largest_contigs = map(lambda x: int(x),sorted(nlargest(1000, cont_lengths_list)))
- #print largest_contigs
- #sorted_lengths = sorted(cont_lengths_list)
-
- min_ctg_length = min(largest_contigs)
- max_isize = int(max(ins_size_reads))
- adjusted_distribution = [0]*int(max_isize+1)
- ## Make hasmap of the number of contigs and their sum
- ## that is larger than a given isize
- current_sum_ctgs = sum(largest_contigs)
- current_nr_ctgs = len(largest_contigs)
- ctgs_larger_than = [] # array indexed by isize, item is tuple is a tuple (n_ctgs, their nucleotide sum)
-
- ctgs_larger_than.append( (current_nr_ctgs, current_sum_ctgs) )
- current_smallest_contig = largest_contigs[0]
- current_smallest_contig_index = 0
- upper_isize = min(max_isize+1, largest_contigs[-1])
- for isize in xrange(upper_isize):
- if isize <= current_smallest_contig:
- ctgs_larger_than.append( (current_nr_ctgs, current_sum_ctgs) )
- else:
- #current_smallest_contig_index += 1
- while isize > largest_contigs[current_smallest_contig_index]:
- current_smallest_contig_index += 1
- current_nr_ctgs -= 1
- current_sum_ctgs -= current_smallest_contig
-
- ctgs_larger_than.append( (current_nr_ctgs, current_sum_ctgs) )
- current_smallest_contig = largest_contigs[current_smallest_contig_index]
-
- # print min_ctg_length, max_isize
- # print ctgs_larger_than
- for o in ins_size_reads:
- obs = int(o)
- if obs > upper_isize:
- continue
- nr_ctgs = ctgs_larger_than[obs][0]
- sum_ctgs = ctgs_larger_than[obs][1]
- w = float(max(sum_ctgs - (obs-1)*nr_ctgs, 10000))
- adjusted_distribution[obs] += 1/w
-
- # if min_ctg_length >= max_isize:
- # for o in ins_size_reads:
- # obs = int(o)
- # w = max(float(sum_ctgs - (obs-1)*nr_ctgs), 1)
- # adjusted_distribution[obs] += 1/w
-
- tot_density = float(sum(adjusted_distribution))
- cum_sum = 0
- curr_isize = 0
- median_density = tot_density/2.0
- while cum_sum <= median_density:
- cum_sum += adjusted_distribution[curr_isize]
- curr_isize +=1
-
- median_adj = curr_isize
-
- if param.plots:
- plots.histogram(ins_size_reads, param, bins=100, x_label='fragment length', y_label='frequency', title='Frag_length_distribuion' + '.' + param.bamfile.split('/')[-1])
- plots.dot_plot(range(len(adjusted_distribution)), adjusted_distribution, param, x_label='fragment length', y_label='frequency', title='Frag_length_distribuion_adjusted' + '.' + param.bamfile.split('/')[-1], set_marker= '.')
-
- ## find a stable mode of the fitted distribution since our distribution is a sample.
- ## It is not very stable just to chose the isize with the highest count
- mode_for_different_windows = []
- for chunk_size in range(1,102, 5):
- adj_distr_chunked = list(sum_chunks(adjusted_distribution, chunk_size))
- mode_adj = (argmax(adj_distr_chunked) + 0.5)*chunk_size
- mode_for_different_windows.append(int(mode_adj))
- print >> Information, "mode for chunk size ", chunk_size, " : ", mode_adj
- mode_adj = sorted(mode_for_different_windows)[int(len(mode_for_different_windows)/2)]
- print "Choosing mode:", mode_adj
-
- #mode_adj = argmax(adjusted_distribution)
- mu_adj = sum(map(lambda (i, f_x): i*f_x, enumerate(adjusted_distribution)))/tot_density
- sigma_adj = math.sqrt(sum(map(lambda (i, f_x): (i-mu_adj)**2 * f_x, enumerate(adjusted_distribution))) / tot_density)
- m_3 = sum(map(lambda (i, f_x): (i-mu_adj)**3 * f_x, enumerate(adjusted_distribution))) / tot_density
-
- # m_3 = sum(map(lambda x: (x - mean_isize) ** 3, ins_size_reads))/n
- skew_adj = m_3 / sigma_adj**3
-
- print 'mu_adjusted:{0}, sigma_adjusted:{1}, skewness_adjusted:{2}'.format(mu_adj, sigma_adj, skew_adj)
- return adjusted_distribution, mu_adj, sigma_adj, skew_adj, median_adj, mode_adj
-#with pysam.Samfile(param.bamfile, 'rb') as bam_file:
-
-def get_metrics(bam_file, param, Information):
- #informative_pair = set([147, 163]) #161,145,129,177,
- cont_names = bam_file.references
- cont_lengths = bam_file.lengths
- #cont_lengths=[int(nr) for nr in cont_lengths] #convert long to int object
- cont_lengths_list = list(cont_lengths)
- indexes = [i for i in range(0, len(cont_lengths_list))]
- largest_contigs_indexes = set(nlargest(1000, indexes, key=lambda i: cont_lengths_list[i])) #get indexes of the 1000 longest contigs
-
- param.lognormal = False #default as False, but cna change below dependant on skew
-
- try:
- bam_file.fetch(cont_names[0])
- except ValueError:
- sys.stderr.write('Need indexed bamfiles, index file should be located in the same directory as the BAM file\nterminating..\n')
- sys.exit(0)
- #largest_contigs_indexes = nlargest(1000, indexes, key=lambda i: cont_lengths_list[i]) #get indexes of the 1000 longest contigs
-
- #print largest_contigs_indexes
-
- if not param.read_len: # user has not specified read len
- #get read length
- nr_reads = 0
- tot_read_len = 0
- # for index in largest_contigs_indexes:
- # try:
- # iter_ = bam_file.fetch(cont_names[index])
- # except ValueError:
- # sys.stderr.write('Need indexed bamfiles, index file should be located in the same directory as the BAM file\nterminating..\n')
- # sys.exit(0)
-
- for read in bam_file:
- if read.rlen != 0:
- tot_read_len += read.rlen
- nr_reads += 1
- else:
- tot_read_len += read.alen
- nr_reads += 1
- if nr_reads >= 100:
- param.read_len = tot_read_len / float(nr_reads)
- break
- else:
- sys.stderr.write('Did not get sufficient readmappings to calculate\
- read_length from mappings. Got {0} mappings. Please provide this parameter or more importantly\
- check why almost no reads are mapping to the contigs.\nterminating..\n'.format(nr_reads))
- sys.exit(0)
-
- bam_file.reset()
-
- if param.mean_ins_size and param.std_dev_ins_size and not param.ins_size_threshold: # user has specified mean and std dev but no thresholds
- param.ins_size_threshold = param.mean_ins_size + 4 * param.std_dev_ins_size
- if param.extend_paths:
- param.contig_threshold = param.ins_size_threshold
- else:
- param.contig_threshold = param.mean_ins_size + (param.std_dev_ins_size / float(param.mean_ins_size)) * param.std_dev_ins_size
- print >> Information, '-T', param.ins_size_threshold, '-t', param.contig_threshold
-
- if not param.mean_ins_size: # user has not specified mean and std dev. (and no thresholds)
- #total_reads_iterated_through = 0
- counter = 1
- ins_size_reads = []
- # for index in largest_contigs_indexes:
- # try:
- # iter_ = bam_file.fetch(cont_names[index])
- # except ValueError:
- # sys.stderr.write('Need indexed bamfiles, index file should be located in the same directory as the BAM file\nterminating..\n')
- # sys.exit(0)
- for read in bam_file:
- if param.orientation == 'fr' and bam_parser.is_proper_aligned_unique_innie(read):
- if read.rname in largest_contigs_indexes:
- ins_size_reads.append(abs(read.tlen))
- counter += 1
- if param.orientation == 'rf' and bam_parser.is_proper_aligned_unique_outie(read):
- if read.rname in largest_contigs_indexes:
- ins_size_reads.append(abs(read.tlen) + 2*param.read_len)
- counter += 1
- if counter > 1000000:
- break
- bam_file.reset()
- # if counter > 1000000:
- # break
-
- #get mean and std dev here.
- #Assure that there were enough reads for computation of mean and variance
- if len(ins_size_reads) <= 1000:
- sys.stderr.write('To few valid read alignments exists to compute mean and variance of library (need at least 1000 observations). Got only ' + str(len(ins_size_reads)) + ' valid alignments. Please specify -m and -s to the program. \nPrinting out scaffolds produced in earlier steps...')
- sys.stderr.write('\nterminating...\n')
- sys.exit(0)
-
- ## SMOOTH OUT THE MEAN HERE by removing extreme observations##
- n = float(len(ins_size_reads))
- mean_isize = sum(ins_size_reads) / n
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), ins_size_reads))) / (n - 1)) ** 0.5
- print >> Information, 'Mean before filtering :', mean_isize
- print >> Information, 'Std_est before filtering: ', std_dev_isize
- extreme_obs_occur = True
- while extreme_obs_occur:
- extreme_obs_occur, filtered_list = AdjustInsertsizeDist(mean_isize, std_dev_isize, ins_size_reads)
- n = float(len(filtered_list))
- mean_isize = sum(filtered_list) / n
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), filtered_list))) / (n - 1)) ** 0.5
- ins_size_reads = filtered_list
-
- n = float(len(ins_size_reads))
- mean_isize = sum(ins_size_reads) / n
- std_dev_isize = (sum(list(map((lambda x: x ** 2 - 2 * x * mean_isize + mean_isize ** 2), ins_size_reads))) / (n - 1)) ** 0.5
-
- print >> Information, 'Mean converged:', mean_isize
- print >> Information, 'Std_est converged: ', std_dev_isize
-
- param.mean_ins_size = mean_isize
- param.std_dev_ins_size = std_dev_isize
-
- m_3 = sum(map(lambda x: (x - mean_isize) ** 3, ins_size_reads))/n
- skewness = m_3 / std_dev_isize**3
- param.skewness = skewness
- print >> Information, 'Skewness of distribution: ', param.skewness
-
- # weight each observation with how likely it is to see it
- adj_distr, mu_adj, sigma_adj, skew_adj, median_adj, mode_adj = getdistr(ins_size_reads, cont_lengths_list, param, Information)
- param.skew_adj = skew_adj
- print >> Information, 'Mean of getdistr adjusted distribution: ', mu_adj
- print >> Information, 'Sigma of getdistr adjusted distribution: ', sigma_adj
- print >> Information, 'Skewness of getdistr adjusted distribution: ', skew_adj
- print >> Information, 'Median of getdistr adjusted distribution: ', median_adj
- print >> Information, 'Mode of getdistr adjusted distribution: ', mode_adj
- print >> Information, 'Using mean and stddev of getdistr adjusted distribution from here: ', mu_adj, sigma_adj
- param.mean_ins_size = mu_adj
- param.std_dev_ins_size = sigma_adj
-
- #### If skewness (of original - not the getdistr)is positive and larger than 0.5
- #### (big enough skew to have impact), we fit to the lognormal distribution
- if param.skew_adj > 0.5:
-
- ###################################################
- #### NOTE: Fitting lognormal of original sample, not getdistr adjusted for
- #### smaller isizes observation bias
- #### because I don't know how yet. If the two distributions are not too unsimilar
- #### it should be a good approximation in practice
- # median = sorted(ins_size_reads)[len(ins_size_reads)/2]
- # mode = mean_isize - 3*(mean_isize - median)
- # print >> Information, 'Mode on initial sample (not getdistr adjusted): ', mode
- # print >> Information, "Median on initial sample (not getdistr adjusted)", median
- # print "mode:", mode
- # print "median", median
- # param.lognormal_mean = math.log(median)
- # param.lognormal_sigma = math.sqrt(param.lognormal_mean - math.log(mode))
- # print >> Information, 'Lognormal mean (not getdistr adjusted): ', param.lognormal_mean
- # print >> Information, "Lognormal stddev (not getdistr adjusted)", param.lognormal_sigma
- #################################################
-
- ## the statistics for the getdistr adjusted distribution
- #mode_adj = mu_adj - 3*(mu_adj - median_adj)
- print >> Information, 'Mode on getdistr adjusted: ', mode_adj
- print >> Information, "Median on getdistr adjusted:", median_adj
- print "mode adj:", mode_adj
- print "median adj", median_adj
- param.lognormal_mean = math.log(median_adj)
- param.lognormal_sigma = math.sqrt(param.lognormal_mean - math.log(mode_adj))
- print >> Information, 'Lognormal mean getdistr adjusted: ', param.lognormal_mean
- print >> Information, "Lognormal stddev getdistr adjusted", param.lognormal_sigma
-
- param.lognormal = True
- #sys.exit()
-
- # TODO: calculate skew of contamination distribution
-
- # stddev_fit = (sum(map(lambda x: (x - mode)**2 , ins_size_reads))/n)**0.5
- # print stddev_fit
-
- # import matplotlib.pyplot as plt
- # plt.hist(ins_size_reads,100)
- # plt.savefig("/Users/ksahlin/_tmp/BESST_ILP/ARABI_27_statistical_score_no_paths/isize_plot")
- else:
- total_reads_iterated_through = None
-
- if not param.ins_size_threshold:
- param.ins_size_threshold = param.mean_ins_size + 4 * param.std_dev_ins_size
- if param.extend_paths:
- param.contig_threshold = param.ins_size_threshold
- else:
- param.contig_threshold = param.mean_ins_size + (param.std_dev_ins_size / float(param.mean_ins_size)) * param.std_dev_ins_size
-
- ## finally, get a reverse complemented read contamination distribution from the MP library if it exists
- n_contamine = get_contamination_metrics(largest_contigs_indexes,bam_file, cont_names, param, Information)
-
-
- print >> Information, ''
- print >> Information, 'LIBRARY STATISTICS'
- print >> Information, 'Mean of library set to:', param.mean_ins_size
- print >> Information, 'Standard deviation of library set to: ', param.std_dev_ins_size
- print >> Information, 'MP library PE contamination:'
- print >> Information, 'Contamine rate (rev comp oriented) estimated to: ', param.contamination_ratio
- print >> Information, 'lib contamine mean (avg fragmentation size): ', param.contamination_mean
- print >> Information, 'lib contamine stddev: ', param.contamination_stddev
- print >> Information, 'Number of contamined reads used for this calculation: ', n_contamine
-
-
- print >> Information, '-T (library insert size threshold) set to: ', param.ins_size_threshold
- print >> Information, '-k set to (Scaffolding with contigs larger than): ', param.contig_threshold
- print >> Information, 'Number of links required to create an edge: ', param.edgesupport
- print >> Information, 'Read length set to: ', param.read_len
- print >> Information, ''
- return()
-
-
- #### Get parameters -r, -m, -s, -T, -t for library ####
- #print >> Information, 'Computing parameters not set by user...'
- #GetParams(bam_file, param, Information)
diff --git a/external/gatb-minia-pipeline/BESST/BESST/lp_solve.py b/external/gatb-minia-pipeline/BESST/BESST/lp_solve.py
deleted file mode 100644
index 8a91a09aa11bac5e94994fdc74e2bb1b1b29c0e9..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/lp_solve.py
+++ /dev/null
@@ -1,250 +0,0 @@
-# Translated from Octave code at:
-# http://www.ecs.shimane-u.ac.jp/~kyoshida/lpeng.htm
-# and placed under MIT licence by Enzo Michelangeli with permission explicitly
-# granted by the original author, Prof. Kazunobu Yoshida
-#
-# -----------------------------------------------------------------------------
-# Copyright (c) 2010, Kazunobu Yoshida, Shimane University, and Enzo Michelangeli,
-# IT Vision Limited
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-# -----------------------------------------------------------------------------
-
-from numpy import *
-
-class Result(dict):
- """ Represents the optimization result.
-
- Attributes
- ----------
- x : ndarray
- The solution of the optimization.
- success : bool
- Whether or not the optimizer exited successfully.
- status : int
- Termination status of the optimizer. Its value depends on the
- underlying solver. Refer to `message` for details.
- message : str
- Description of the cause of the termination.
- fun, jac, hess : ndarray
- Values of objective function, Jacobian and Hessian (if available).
- nfev, njev, nhev: int
- Number of evaluations of the objective functions and of its
- Jacobian and Hessian.
- nit: int
- Number of iterations performed by the optimizer.
-
- Notes
- -----
- There may be additional attributes not listed above depending of the
- specific solver. Since this class is essentially a subclass of dict
- with attribute accessors, one can see which attributes are available
- using the `keys()` method.
- """
- def __getattr__(self, name):
- try:
- return self[name]
- except KeyError:
- raise AttributeError(name)
-
- __setattr__ = dict.__setitem__
- __delattr__ = dict.__delitem__
-
- def __repr__(self):
- if self.keys():
- m = max(map(len, self.keys())) + 1
- return '\n'.join([k.rjust(m) + ': ' + repr(v)
- for k, v in self.iteritems()])
- else:
- return self.__class__.__name__ + "()"
-
-
-class LPResult(Result):
- """
- Solution to a linear programming problem
-
- Attributes
- ----------
- x : ndarray
- The solution of the optimization.
- success : bool
- Whether or not the optimizer exited successfully.
- fun : float
- The optimal value
- is_bounded : bool
- True if the solution is bounded; False if unbounded
- is_solvable : bool
- True if the problem is solvable; False if unsolvable
- basis : ndarray
- Indices of the basis of the solution.
- """
- _fields = ['x', 'min', 'is_bounded', 'solvable', 'basis']
-
-def lp_solve(c, A, b, tol=1e-10):
- """
- Solves a linear programming problem using a two-phase method.
-
- The problem solved is::
-
- minimize z = c' x
- subject to A x = b, x >= 0
-
- Parameters
- ----------
- c : array_like
- A : array_like
- b : array_like
- Problem parameters
- tol : float, optional
- Tolerance
-
- Returns
- -------
- sol : LPResult
- A solution object, with the properties:
- x : ndarray
- An optimal solution.
- fun : float
- The optimal value.
- is_bounded : bool
- True if the solution is bounded; False if unbounded.
- is_solvable : bool
- True if the problem is solvable; False if unsolvable.
- basis : ndarray
- Indices of the basis of the solution.
-
- Notes
- -----
- The solution is found using the two phase method, where the
- simplex method is used at each stage.
-
- """
- c = asarray(c)
- A = asarray(A)
- b = asarray(b)
-
- m,n = A.shape # m: number of constraints; n: number of variables
- for i in xrange(m):
- if b[i] < 0.0:
- A[i,:] = -A[i,:]
- b[i] = -b[i]
- d = -sum(A, axis=0)
- w0 = sum(b)
- H = vstack([ # The initial simplex table of phase one
- hstack([A, array([b]).T]), # first m rows
- hstack([c, 0.]), # last-but-one
- hstack([d, -w0])]) # last
- indx = range(n)
- basis = arange(n, n+m) # m elements from n to n+m-1
- is_bounded = _simplex(H, basis, indx, 1)
- if H[m+1,n] < -tol: # last row, last column
- sol = False
- optx = None
- zmin = None
- is_bounded = None
- else:
- sol = True
- j = -1
- for i in xrange(n):
- j = j+1
- if H[m+1,j] > tol:
- H = delete(H, j, 1) # H[:,j] = [] # delete column j from H
- del indx[j]
- j = j-1
- H = delete(H, m+1, 0)
- if indx > 0:
- # Phase two
- is_bounded = _simplex(H,basis,indx,2)
- if is_bounded:
- optx = zeros(n+m)
- for i in xrange(m):
- optx[basis[i]] = H[i,-1]
- optx = optx[0:n]
- zmin = -H[-1,-1] # last row, last column
- else:
- optx = None
- zmin = -Inf
- else:
- optx = zeros(n)
- zmin = 0
-
- return LPResult(x=optx,
- fun=zmin,
- success=(sol and is_bounded),
- is_bounded=is_bounded,
- is_solvable=sol,
- basis=basis)
-
-def _simplex(H,basis,indx,s):
- '''
- [H1,basis,is_bounded] = _simplex(H,basis,indx,s)
- H: simplex table (MODIFIED).
- basis: the indices of basis (MODIFIED).
- indx: the indices of x.
- s: 1 for phase one; 2 for phase two.
- H1: new simplex table.
- is_bounded: True if the solution is bounded; False if unbounded.
- '''
- if s == 1:
- s0 = 2
- elif s == 2:
- s0 = 1
- n1 = H.shape[0]
- sol = False
- while not sol:
- q = H[-1, :-1] # last row, all columns but last
- jp = argmin(q)
- fm = q[jp]
- if fm >= 0:
- is_bounded = True # bounded solution
- sol = True
- else:
- q = H[:-s0,jp]
- ip = argmax(q)
- hm = q[ip]
- if hm <= 0:
- is_bounded = False # unbounded solution
- sol = True
- else:
- h1 = zeros(n1-s0)
- for i in xrange(n1-s0):
- if H[i,jp] > 0:
- h1[i] = H[i,-1]/H[i,jp]
- else:
- h1[i] = Inf
- ip = argmin(h1)
- minh1 = h1[ip]
- basis[ip] = indx[jp]
- if not _pivot(H,ip,jp):
- raise ValueError("the first parameter is a Singular matrix")
- return is_bounded
-
-def _pivot(H,ip,jp):
- # H is MODIFIED
- n, m = H.shape
- piv = H[ip,jp]
- if piv == 0:
- #print('singular')
- return False
- else:
- H[ip,:] /= piv
- for i in xrange(n):
- if i != ip:
- H[i,:] -= H[i,jp]*H[ip,:]
- return True
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/BESST/BESST/main.py b/external/gatb-minia-pipeline/BESST/BESST/main.py
deleted file mode 100644
index 674a23a560721e7c17c288af9578f76dc3ffb905..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/main.py
+++ /dev/null
@@ -1,5 +0,0 @@
-'''
-Created on Jun 14, 2013
-
-@author: ksahlin
-'''
diff --git a/external/gatb-minia-pipeline/BESST/BESST/order_contigs.py b/external/gatb-minia-pipeline/BESST/BESST/order_contigs.py
deleted file mode 100644
index 6867cfd20f49b686b3c40dd9917522075490a524..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/order_contigs.py
+++ /dev/null
@@ -1,587 +0,0 @@
-'''
- Created on May 30, 2014
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-import copy
-import math
-import random
-from collections import Counter
-import cPickle
-import os
-import subprocess
-import mathstats.log_normal_param_est as lnpe
-
-
-#import numpy as np
-
-
-from mathstats.normaldist.normal import normpdf
-from mathstats.normaldist.truncatedskewed import param_est as GC
-
-from BESST.lp_solve import lp_solve
-
-
-class LpForm(object):
- """docstring for LpForm"""
- def __init__(self):
- super(LpForm, self).__init__()
- self.rows = []
- self.b = []
-
- def add_objective(self, obj):
- self.obj = obj
-
- def add_constraint(self, expression, value):
- self.rows.append(expression)
- self.b.append(value)
-
- def standard_form(self):
- """
- Converts Ax' <=b
- to Ax = b, b >= 0
- by introducing slack/surplus variables
- """
-
- A = []
- c = []
-
- # build full tableau and convert to normal form if negative constants
- tot_slack_variables = len(self.rows)
-
- for i in range(len(self.rows)):
- ident = [0 for r in range(len(self.rows))]
-
- # if negative constant
- if self.b[i] < 0:
- # add a surplus variable
- ident[i] = -1
- #reverse all other values
- self.rows[i] = [ -k for k in self.rows[i] ]
- self.rows[i] += ident
- # change sign of constant
- self.b[i] = -self.b[i]
-
- # if positive constant
- else:
- # add a slack varaible
- ident[i] = 1
- self.rows[i] += ident
-
- A = self.rows
-
- c = self.obj + [0]*tot_slack_variables
- return A, self.b, c
-
-
-class Contig(object):
- """Container with contig information for a contig in a path"""
- def __init__(self, index, length):
- super(Contig, self).__init__()
- self.index = index
- self.length = length
- self.position = None
-
-
-class Path(object):
- """Contains all information of a path. This is basically a supgraph of the
- Scaffold graph in BESST contianing all contigs in a path that has high score
- and is going to be made into a scaffold.
-
- Path is an object with methods for calculating likelihood of a path given link observations.
- Due to computational requiremants, we don't calculate the true likelihoos all paths usually have thousands
- of links. Instead, we take the average link obervation between all contigs. This will not give true ML
- estimates but speeds up calculation with thousands of x order. In practice, using average link obervation
- For ML estimation will give a fairly good prediction. For this cheat, see comment approx 15 lines below. """
- def __init__(self, ctg_lengths, observations, param):
- super(Path, self).__init__()
- self.mean = param.mean_ins_size
- self.stddev = param.std_dev_ins_size
- self.read_len = param.read_len
- self.contamination_ratio = param.contamination_ratio
- self.contamination_mean = param.contamination_mean
- self.contamination_stddev = param.contamination_stddev
- self.ctgs = []
- self.ctg_lengths = ctg_lengths
- for i,length in enumerate(ctg_lengths):
- self.ctgs.append(Contig(i, length))
- self.ctgs = tuple(self.ctgs)
- self.gaps = [0]*(len(ctg_lengths)-1) # n contigs has n-1 gaps between them, start with gap size 0
-
- # get positions for when all gaps are 0
- self.update_positions()
-
- # let us cheat here! Instead of calculating likeliooods of thousands of
- # onservations we calculate the ikelihood for them average (mean) of the
- # observations and weight it with the number of observations
- self.mp_links = 0.0
- self.pe_links = 0.0
- obs_dict = {}
-
-
- if all(length in self.ctg_lengths for length in [670, 2093]) or all(length in self.ctg_lengths for length in [900, 3810]) or all(length in self.ctg_lengths for length in [2528, 591]) or all(length in self.ctg_lengths for length in [734, 257, 1548]):
- print >> param.information_file, ''
- print >> param.information_file, ''
- print >> param.information_file, 'Setting up path', ctg_lengths
- for c1,c2,is_PE_link in observations:
- mean_obs, nr_obs, stddev_obs, list_of_obs = observations[(c1,c2,is_PE_link)]
- if is_PE_link:
- mean_PE_obs = self.ctgs[c1].length + self.ctgs[c2].length - observations[(c1,c2,is_PE_link)][0] + 2*param.read_len
- list_of_obs = [ self.ctgs[c1].length + self.ctgs[c2].length - obs + 2*param.read_len for obs in list_of_obs]
- print >> param.information_file, 'PE LINK, mean obs:', mean_PE_obs, 'stddev obs:', stddev_obs, 'nr obs:', nr_obs, 'c1 length', self.ctgs[c1].length, 'c2 length', self.ctgs[c2].length
- obs_dict[(c1, c2, is_PE_link)] = (mean_PE_obs, nr_obs, stddev_obs, list_of_obs)
- self.pe_links += nr_obs
- # if mean_PE_obs > self.contamination_mean + 6 * self.contamination_stddev:
- # self.observations = None
- # return None
- else:
- #mean_obs = sum(observations[(c1,c2,is_PE_link)])/nr_obs
- print >> param.information_file, 'MP LINK, mean obs:', mean_obs, 'stddev obs:', stddev_obs, 'nr obs:', nr_obs, 'c1 length', self.ctgs[c1].length, 'c2 length', self.ctgs[c2].length
-
- obs_dict[(c1, c2, is_PE_link)] = (mean_obs, nr_obs, stddev_obs, list_of_obs)
- self.mp_links += nr_obs
- print >> param.information_file, ''
- print >> param.information_file, ''
-
-
- for c1,c2,is_PE_link in observations:
- #nr_obs = len(observations[(c1,c2,is_PE_link)])
- mean_obs, nr_obs, stddev_obs, list_of_obs = observations[(c1,c2,is_PE_link)]
- if is_PE_link:
- mean_PE_obs = self.ctgs[c1].length + self.ctgs[c2].length - observations[(c1,c2,is_PE_link)][0] + 2*param.read_len
- list_of_obs = [ self.ctgs[c1].length + self.ctgs[c2].length - obs + 2*param.read_len for obs in list_of_obs]
- #PE_obs = map(lambda x: self.ctgs[c1].length + self.ctgs[c2].length - x + 2*param.read_len ,observations[(c1,c2,is_PE_link)])
- #mean_obs = sum( PE_obs)/nr_obs
- obs_dict[(c1, c2, is_PE_link)] = (mean_PE_obs, nr_obs, stddev_obs, list_of_obs)
- self.pe_links += nr_obs
- # if mean_PE_obs > self.contamination_mean + 6 * self.contamination_stddev and not initial_path:
- # self.observations = None
- # return None
- else:
- #mean_obs = sum(observations[(c1,c2,is_PE_link)])/nr_obs
- obs_dict[(c1, c2, is_PE_link)] = (mean_obs, nr_obs, stddev_obs, list_of_obs)
- self.mp_links += nr_obs
-
-
- self.observations = obs_dict
- #print self.observations
-
-
- # for c1,c2 in self.observations:
- # if self.observations[(c1,c2)][0] > 1500:
- # print self.observations
-
-
- def get_distance(self,start_index,stop_index):
- total_contig_length = sum(map(lambda x: x.length ,filter(lambda x: start_index <= x.index < stop_index, self.ctgs) ))
- total_gap_length = sum(self.gaps[start_index:stop_index])
- index_adjusting = len(self.gaps[start_index:stop_index]) # one extra bp shifted each time
- return (total_contig_length, total_gap_length, index_adjusting)
-
- def update_positions(self):
- for ctg in self.ctgs:
- index = ctg.index
- ctg.position = sum(self.get_distance(0,index))
-
- # def get_inferred_isizes(self):
- # self.isizes = {}
-
- # for (c1,c2,is_PE_link) in self.observations:
- # gap = self.ctgs[c2].position - (self.ctgs[c1].position + self.ctgs[c1].length) - (c2-c1) # last thing is an index thing
- # #x = map(lambda obs: obs[0] + gap , self.observations[(c1,c2)]) # inferr isizes
- # x = self.observations[(c1,c2,is_PE_link)][0] + gap
- # self.isizes[(c1,c2,is_PE_link)] = x
-
- # def get_GapEst_isizes(self):
- # self.gapest_predictions = {}
- # for (i,j,is_PE_link) in self.observations:
- # mean_obs = self.observations[(i,j,is_PE_link)][0]
- # if is_PE_link:
- # self.gapest_predictions[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + GC.GapEstimator(self.contamination_mean, self.contamination_stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- # else:
- # self.gapest_predictions[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
- # #print mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
-
-
- # def new_state_for_ordered_search(self,start_contig,stop_contig,mean,stddev):
- # """
- # This function gives a new state between two contigs c1 and c2 in the contig path
- # that we will change the gap size for.
- # Currently, we change the gap to expected_mean_obs - mean_observation, e.g. a
- # semi-naive estimation. More variablity in gap prediction could be acheved in the
- # same way as described for function propose_new_state_MCMC().
-
- # """
- # new_path = copy.deepcopy(self) # create a new state
- # (c1,c2) = (start_contig,stop_contig)
- # mean_obs = self.observations[(c1,c2,0)][0] if (c1,c2,0) in self.observations else self.observations[(c1,c2,1)][0] # take out observations and
- # exp_mean_over_bp = mean + stddev**2/float(mean+1)
- # proposed_distance = exp_mean_over_bp - mean_obs # choose what value to set between c1 and c2
-
- # #print 'CHOSEN:', (c1,c2), 'mean_obs:', mean_obs, 'proposed distance:', proposed_distance
- # (total_contig_length, total_gap_length, index_adjusting) = self.get_distance(c1+1,c2)
- # #print 'total ctg length, gap_lenght,index adjust', (total_contig_length, total_gap_length, index_adjusting)
- # avg_suggested_gap = (proposed_distance - total_contig_length) / (c2-c1)
- # #print avg_suggested_gap, proposed_distance, total_contig_length, c2-c1
- # for index in range(c1,c2):
- # new_path.gaps[index] = avg_suggested_gap
- # #new_path.gaps[index] = proposed_distance
- # return new_path
-
-
- # def calc_log_likelihood(self,mean,stddev):
- # log_likelihood_value = 0
- # exp_mean_over_bp = mean + stddev**2/float(mean+1)
- # for (c1,c2) in self.isizes:
- # log_likelihood_value += math.log( normpdf(self.isizes[(c1,c2)],exp_mean_over_bp, stddev) ) * self.observations[(c1,c2)][1]
- # #for isize in self.isizes[(c1,c2)]:
- # # log_likelihood_value += math.log( normpdf(isize,mean,stddev) )
-
- # return log_likelihood_value
-
- # def calc_dist_objective(self):
- # objective_value = 0
- # self.get_GapEst_isizes()
- # for (c1,c2, is_PE_link) in self.isizes:
- # objective_value += abs(self.gapest_predictions[(c1,c2,is_PE_link)] - self.isizes[(c1,c2,is_PE_link)]) * self.observations[(c1,c2,is_PE_link)][1]
- # #for isize in self.isizes[(c1,c2)]:
- # # objective_value += math.log( normpdf(isize,mean,stddev) )
-
- # return objective_value
-
- def make_path_dict_for_besst(self):
- path_dict = {}
- for ctg1,ctg2 in zip(self.ctgs[:-1],self.ctgs[1:]):
- path_dict[(ctg1,ctg2)] = ctg2.position - (ctg1.position + ctg1.length) - 1
- #print path_dict
- return path_dict
-
-
- # def calc_probability_of_LP_solution(self, help_variables):
- # log_prob = 0
- # for (i,j,is_PE_link),variable in help_variables.iteritems():
- # print self.contamination_ratio * self.observations[(i,j,is_PE_link)][1] * normpdf(variable.varValue,self.contamination_mean,self.contamination_stddev)
- # if is_PE_link:
- # try:
- # log_prob += math.log(self.contamination_ratio * self.observations[(i,j,is_PE_link)][1] * normpdf(variable.varValue,self.contamination_mean,self.contamination_stddev))
- # except ValueError:
- # log_prob += - float("inf")
- # else:
- # try:
- # log_prob += math.log((1 - self.contamination_ratio) * self.observations[(i,j,is_PE_link)][1]* normpdf(variable.varValue,self.contamination_mean,self.contamination_stddev))
- # except ValueError:
- # log_prob += - float("inf")
- # return log_prob
-
- def LP_solve_gaps(self,param):
- exp_means_gapest = {}
-
- for (i,j,is_PE_link) in self.observations:
- mean_obs = self.observations[(i,j,is_PE_link)][0]
- if is_PE_link:
- exp_means_gapest[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + GC.GapEstimator(self.contamination_mean, self.contamination_stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- #print 'GAPEST:',mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.contamination_mean, self.contamination_stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
- else:
- if param.lognormal:
- samples = self.observations[(i,j,is_PE_link)][3]
- exp_means_gapest[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + lnpe.GapEstimator(param.lognormal_mean, param.lognormal_sigma, self.read_len, samples, self.ctgs[i].length, c2_len=self.ctgs[j].length)
- else:
- exp_means_gapest[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- #print 'GAPEST:',mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
-
- if all(length in self.ctg_lengths for length in [670, 2093]) or all(length in self.ctg_lengths for length in [900, 3810]) or all(length in self.ctg_lengths for length in [2528, 591]) or all(length in self.ctg_lengths for length in [734, 257, 1548]):
-
- for (i,j,is_PE_link) in self.observations:
- mean_obs = self.observations[(i,j,is_PE_link)][0]
- if is_PE_link:
- #exp_means_gapest[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + GC.GapEstimator(self.contamination_mean, self.contamination_stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- print >> param.information_file, 'GAPEST:',mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.contamination_mean, self.contamination_stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
- else:
- #exp_means_gapest[(i,j,is_PE_link)] = self.observations[(i,j,is_PE_link)][0] + GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- print >> param.information_file, 'GAPEST:',mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
-
- ####################
- ####### NEW ########
- ####################
-
- # convert problem to standard form
- # minimize z = c' x
- # subject to A x = b, x >= 0
- # b does not neccessarily need to be a positive vector
-
- # decide how long rows.
- # we need 2*g gap variables because they can be negative
- # and r help variables because absolute sign in objective function
-
- t = LpForm()
-
- g = len(self.ctgs)-1
- r = len(self.observations)
- n = 2*g+r
-
- #A = []
- #c = []
- #b = []
- # add gap variable constraints g_i = x_i - y_i <= mean + 2stddev, x_i,y_i >= 0
- # gap 0 on column 0, gap1 on column 1 etc.
-
- for i in range(g):
- row = [0]*n
- row[2*i] = 1 # x_i
- row[2*i+1] = -1 # y_i
- #A.append(row)
- #b.append(self.mean + 2*self.stddev)
- t.add_constraint(row, self.mean + 2*self.stddev)
-
- # add r help variable constraints (for one case in absolute value)
- for h_index,(i,j,is_PE_link) in enumerate(self.observations):
- row = [0]*n
-
- # g gap variable constants
- for k in range(n):
- if i<= k <j:
- row[2*k] = -1
- row[2*k+1] = 1
-
- # r Help variables
- row[ 2*g + h_index] = -1
-
- # sum of "inbetween" contig lengths + observation
- constant = sum(map(lambda x: x.length, self.ctgs[i+1:j])) + self.observations[(i,j,is_PE_link)][0]
- predicted_distance = exp_means_gapest[(i,j,is_PE_link)]
-
- t.add_constraint(row, constant - predicted_distance)
-
- # add r help variable constraints (for the other case in absolute value)
- for h_index,(i,j,is_PE_link) in enumerate(self.observations):
- row = [0]*n
-
- # q gap variable constants
- for k in range(n):
- if i<= k <j:
- row[2*k] = 1
- row[2*k+1] = -1
-
- # r Help variables
- row[ 2*g + h_index] = -1
-
- # sum of "inbetween" contig lengths + observation
- constant = sum(map(lambda x: x.length, self.ctgs[i+1:j])) + self.observations[(i,j,is_PE_link)][0]
- predicted_distance = exp_means_gapest[(i,j,is_PE_link)]
-
- t.add_constraint(row, predicted_distance - constant )
-
- # add objective row
-
- # calculate the total penalties of discrepancies of stddevs given assigned orientations
- # of all edges
- obj_delta_stddev = 0
- if self.contamination_ratio:
- obj_row = [0]*n
- for h_index,(i,j,is_PE_link) in enumerate(self.observations):
- n = self.observations[(i,j,is_PE_link)][1]
- obs_stddev = self.observations[(i,j,is_PE_link)][2]
- if is_PE_link:
- obj_delta_stddev += abs(self.contamination_stddev - obs_stddev) * n
- else:
- obj_delta_stddev += abs(self.stddev - obs_stddev) * n
-
- obj_row[ 2*g + h_index] = is_PE_link * n + (1-is_PE_link) * n
- #obj_row[ 2*g + h_index] = is_PE_link*self.stddev*n + (1-is_PE_link)*self.contamination_stddev * n
-
- #obj_row[ 2*g + h_index] = is_PE_link * self.stddev * self.observations[(i,j,is_PE_link)][1] + (1-is_PE_link) * self.contamination_stddev * self.observations[(i,j,is_PE_link)][1]
- # obj_row[ 2*g + h_index] = is_PE_link * self.stddev * (1 - self.contamination_ratio) * self.observations[(i,j,is_PE_link)][1] + (1-is_PE_link) * self.contamination_stddev * (self.contamination_ratio)*self.observations[(i,j,is_PE_link)][1]
- t.add_objective(obj_row)
- else:
- obj_row = [0]*n
- for h_index,(i,j,is_PE_link) in enumerate(self.observations):
- obj_row[ 2*g + h_index] = self.observations[(i,j,is_PE_link)][1]
- t.add_objective(obj_row)
-
- A, b, c = t.standard_form()
-
- # sol_lsq =np.linalg.lstsq(A,b)
- # print "LEAST SQUARES SOLUTION:"
- # print sol_lsq[0]
-
- #t.display()
-
- # print 'Objective:', c
- # for row in A:
- # print 'constraint:', row
- # print 'constnts:', b
- lpsol = lp_solve(c,A,b,tol=1e-4)
- optx = lpsol.x
- # zmin = lpsol.fun
- # bounded = lpsol.is_bounded
- # solvable = lpsol.is_solvable
- # basis = lpsol.basis
- # print " ---->"
- # print "optx:",optx
- # print "zmin:",zmin
- # print "bounded:",bounded
- # print "solvable:",solvable
- # print "basis:",basis
- # print "-------------------------------------------"
-
- # print "LP SOLUTION:"
- # print optx
-
- # transform solutions to gaps back
- gap_solution = []
- for i in range(g):
- gap_solution.append( round (optx[2*i] -optx[2*i +1],0) )
-
- self.objective = lpsol.fun
-
- # also add the penalties from the observed standard deviations
- #self.objective += obj_delta_stddev
-
- # ctg_lengths = map(lambda x: x.length, self.ctgs)
- # if 1359 in ctg_lengths and 673 in ctg_lengths: #len(path.gaps) >= 4:
- # print 'Obj:',self.objective
- # print "of which stddev contributing:", obj_delta_stddev
- #print "objective:",self.objective
-
- #### Use the added accurace from the narrow contamine distribution here
- #### to further precisely adjust the gaps in the LP solution if there is
- #### any pe links
- if self.contamination_ratio:
- for g_i in xrange(g):
- if (g_i, g_i +1, True) in self.observations: # if it is a PE-link
- mean_obs = self.observations[(g_i, g_i+1, True)][0]
- gap_contamination = exp_means_gapest[(g_i, g_i+1, True)] - mean_obs
- old_gap = gap_solution[g_i]
- gap_solution[g_i] = gap_contamination
- #print " changing contamination gap from: {0} to {1}".format(old_gap, gap_contamination)
-
- return gap_solution
-
- def __str__(self):
- string= ''
- for ctg in self.ctgs:
- string += 'c'+str(ctg.index) +',startpos:'+ str(ctg.position)+',endpos:'+str(ctg.position + ctg.length)+'\n'
-
- return string
-
-
-# def ordered_search(path):
-
-# path.get_inferred_isizes()
-
-# for c1 in range(len(path.ctgs)-1):
-# for c2 in range(c1+1,len(path.ctgs)):
-# if (c1,c2) in path.observations:
-# suggested_path = path.new_state_for_ordered_search(c1,c2,path.mean,path.stddev)
-# suggested_path.update_positions()
-# suggested_path.get_inferred_isizes()
-# suggested_path.calc_dist_objective()
-# if suggested_path.calc_dist_objective() < path.calc_dist_objective():
-# #print "SWITCHED PATH TO SUGGESTED PATH!!"
-# path = suggested_path
-# #print path
-# else:
-# pass
-# #print 'PATH not taken!'
-# else:
-# continue
-
-# # print 'FINAL PATH:'
-# # print path
-# # print 'With likelihood: ', path.calc_log_likelihood(mean,stddev)
-
-# return path
-
-
-
-def main(contig_lenghts, observations, param):
- """
- contig_lenghts: Ordered list of integers which is contig lengths (ordered as contigs comes in the path)
- observations: dictionary oflist of observations, eg for contigs c1,c2,c3
- we can have [(c1,c2):[23, 33, 21],(c1,c3):[12,14,11],(c2,c3):[11,34,32]]
- """
-
- path = Path(contig_lenghts,observations, param)
-
- if path.observations == None:
- return None
-
- # ML_path = MCMC(path,mean,stddev)
- # ML_path = ordered_search(path,mean,stddev)
-
- optimal_LP_gaps = path.LP_solve_gaps(param)
- path.gaps = optimal_LP_gaps
- ctg_lengths = map(lambda x: x.length, path.ctgs)
- if all(length in ctg_lengths for length in [670, 2093]) or all(length in ctg_lengths for length in [900, 3810]) or all(length in ctg_lengths for length in [2528, 591]) or all(length in ctg_lengths for length in [734, 257, 1548]): #len(path.gaps) >= 4:
- print >> param.information_file, 'Solution:', path.gaps
- print >> param.information_file, "objective:",path.objective
- print >> param.information_file, 'ctg lengths:', map(lambda x: x.length, path.ctgs)
- print >> param.information_file, 'mp links:', path.mp_links
- print >> param.information_file, 'pe links:', path.pe_links
- print >> param.information_file, 'PE relative freq', path.pe_links / (path.pe_links + path.mp_links)
-
- path.update_positions()
-
- # print 'MCMC path:'
- # print ML_path
- # print 'MCMC path likelihood:',ML_path.calc_log_likelihood(mean,stddev)
- # print 'Ordered search path:'
- # print ML_path
- # print 'Ordered search likelihood:',ML_path.calc_log_likelihood(mean,stddev)
- # return ML_path
-
- return path
-
-if __name__ == '__main__':
- contig_lenghts = [3000,500,500,500,3000]
- observations_normal = {(0,1):[1800,2000], (0,2):[1500,1800,1400,1700], (0,3):[1200,800,1000],
- (1,2):[750,800],(1,3):[600,700], (1,4):[300,600,700],
- (2,3):[700,750], (2,4):[1400,1570],
- (3,4):[2000,1750], }
-
- observations_linear = {(0,1):[450,500], (1,2):[750,800],
- (2,3):[700,750], (3,4):[400,170]}
-
- # The imortance of support:
- # one edge with a lot of observatins contradicting the others
- observations_matter = {(0,1):[450,500], (1,2):[750,800],
- (2,3):[700,750], (3,4):[400,170],
- (0,4):[700]*30 }
-
- # long contig, 500bp gap, 3*short_contigs, long contig
- observations = {(0,1):[1450,1300,1200,1570], (0,2):[700,800,1000], (0,3):[250,300],
- (1,2):[900],(1,3):[900,800], (1,4):[800,900,1000],
- (2,3):[900], (2,4):[900,800],
- (3,4):[1500,1750,1350,1900,1950] }
-
- # negative gaps test case here:
-
-
- mean = 1500
- stddev = 500
- read_len = 100
- main(contig_lenghts,observations,mean,stddev, read_len)
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/pathgaps.py b/external/gatb-minia-pipeline/BESST/BESST/pathgaps.py
deleted file mode 100644
index d7653df19c4a31c85daca8cdea505c1800959165..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/pathgaps.py
+++ /dev/null
@@ -1,424 +0,0 @@
-'''
- Created on May 30, 2014
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-import copy
-import math
-import random
-from collections import Counter
-
-from pulp import *
-from mathstats.normaldist.normal import normpdf
-from mathstats.normaldist.truncatedskewed import param_est as GC
-
-
-
-
-class Contig(object):
- """Container with contig information for a contig in a path"""
- def __init__(self, index, length):
- super(Contig, self).__init__()
- self.index = index
- self.length = length
- self.position = None
-
-
-class Path(object):
- """Contains all information of a path. This is basically a supgraph of the
- Scaffold graph in BESST contianing all contigs in a path that has high score
- and is going to be made into a scaffold.
-
- Path is an object with methods for calculating likelihood of a path given link observations.
- Due to computational requiremants, we don't calculate the true likelihoos all paths usually have thousands
- of links. Instead, we take the average link obervation between all contigs. This will not give true ML
- estimates but speeds up calculation with thousands of x order. In practice, using average link obervation
- For ML estimation will give a fairly good prediction. For this cheat, see comment approx 15 lines below. """
- def __init__(self, ctg_lengths, observations, mean, stddev,read_len):
- super(Path, self).__init__()
- self.mean = mean
- self.stddev = stddev
- self.read_len = read_len
- self.ctgs = []
- for i,length in enumerate(ctg_lengths):
- self.ctgs.append(Contig(i, length))
- self.ctgs = tuple(self.ctgs)
- self.gaps = [0]*(len(ctg_lengths)-1) # n contigs has n-1 gaps between them, start with gap size 0
-
- # get positions for when all gaps are 0
- self.update_positions()
-
- # let us cheat here! Instead of calculating likeliooods of thousands of
- # onservations we calculate the ikelihood for them average (mean) of the
- # observations and weight it with the number of observations
- obs_dict = {}
- for c1,c2 in observations:
- nr_obs = len(observations[(c1,c2)])
- mean_obs = sum(observations[(c1,c2)])/nr_obs
- obs_dict[(c1,c2)] = (mean_obs,nr_obs)
-
-
- self.observations = obs_dict
-
- # for c1,c2 in self.observations:
- # if self.observations[(c1,c2)][0] > 1500:
- # print self.observations
-
-
- def get_distance(self,start_index,stop_index):
- total_contig_length = sum(map(lambda x: x.length ,filter(lambda x: start_index <= x.index < stop_index, self.ctgs) ))
- total_gap_length = sum(self.gaps[start_index:stop_index])
- index_adjusting = len(self.gaps[start_index:stop_index]) # one extra bp shifted each time
- return (total_contig_length, total_gap_length, index_adjusting)
-
- def update_positions(self):
- for ctg in self.ctgs:
- index = ctg.index
- ctg.position = sum(self.get_distance(0,index))
-
- def get_inferred_isizes(self):
- self.isizes = {}
-
- for (c1,c2) in self.observations:
- gap = self.ctgs[c2].position - (self.ctgs[c1].position + self.ctgs[c1].length) - (c2-c1) # last thing is an index thing
- #x = map(lambda obs: obs[0] + gap , self.observations[(c1,c2)]) # inferr isizes
- x = self.observations[(c1,c2)][0] + gap
- self.isizes[(c1,c2)] = x
-
- def get_GapEst_isizes(self):
- self.gapest_predictions = {}
- for (i,j) in self.observations:
- mean_obs = self.observations[(i,j)][0]
- self.gapest_predictions[(i,j)] = self.observations[(i,j)][0] + GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- #print mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
-
- def propose_new_state_MCMC(self,mean,stddev):
- """
- This function proposes (by random sampling) an edge between two contigs c1 and c2 in the contig path
- that we will change the gap size for.
- Currently, we change the gap to expected_mean_obs - mean_observation, e.g. a
- semi-naive estimation. More variablity in the proposal function is required for coming
- closer to true ML gap sizes in a path. This can be achieved for example by, not only
- sampling the edge, but also sample the gap with e.g. a N(expected_mean_obs - mean_observation, stddev/sqrt(nr_obs))
- distribution.
-
- However, getting high accuracy in gap for all contigs in a path can require many samples in the MCMC chain and we have
- many paths to estimate. Also, in practice ML_gap_naive is often a decent proposal.
-
- """
- path_proposed = copy.deepcopy(self) # create a new state
- #(index,gap) = random.choice([(i,gap) for i,gap in enumerate(self.gaps)]) # choose a gap to change
- (c1,c2) = random.choice(self.observations.keys())
- mean_obs = self.observations[(c1,c2)][0] # take out observations and
-
- #obs = self.observations[(index,index+1)] # take out observations and
- exp_mean_over_bp = mean + stddev**2/float(mean+1)
- #mean_obs = sum(obs)/float(len(obs)) # get the mean
- proposed_distance = exp_mean_over_bp - mean_obs # choose what value to set between c1 and c2
- #print 'CHOSEN:', (c1,c2), 'mean_obs:', mean_obs, 'proposed distance:', proposed_distance
- (total_contig_length, total_gap_length, index_adjusting) = self.get_distance(c1+1,c2)
- #print 'total ctg length, gap_lenght,index adjust', (total_contig_length, total_gap_length, index_adjusting)
- avg_suggested_gap = (proposed_distance - total_contig_length) / (c2-c1)
- #print avg_suggested_gap, proposed_distance, total_contig_length, c2-c1
- for index in range(c1,c2):
- path_proposed.gaps[index] = avg_suggested_gap
- #path_proposed.gaps[index] = proposed_distance
- return path_proposed
-
- def new_state_for_ordered_search(self,start_contig,stop_contig,mean,stddev):
- """
- This function gives a new state between two contigs c1 and c2 in the contig path
- that we will change the gap size for.
- Currently, we change the gap to expected_mean_obs - mean_observation, e.g. a
- semi-naive estimation. More variablity in gap prediction could be acheved in the
- same way as described for function propose_new_state_MCMC().
-
- """
- new_path = copy.deepcopy(self) # create a new state
- (c1,c2) = (start_contig,stop_contig)
- mean_obs = self.observations[(c1,c2)][0] # take out observations and
- exp_mean_over_bp = mean + stddev**2/float(mean+1)
- proposed_distance = exp_mean_over_bp - mean_obs # choose what value to set between c1 and c2
-
- #print 'CHOSEN:', (c1,c2), 'mean_obs:', mean_obs, 'proposed distance:', proposed_distance
- (total_contig_length, total_gap_length, index_adjusting) = self.get_distance(c1+1,c2)
- #print 'total ctg length, gap_lenght,index adjust', (total_contig_length, total_gap_length, index_adjusting)
- avg_suggested_gap = (proposed_distance - total_contig_length) / (c2-c1)
- #print avg_suggested_gap, proposed_distance, total_contig_length, c2-c1
- for index in range(c1,c2):
- new_path.gaps[index] = avg_suggested_gap
- #new_path.gaps[index] = proposed_distance
- return new_path
-
-
- def calc_log_likelihood(self,mean,stddev):
- log_likelihood_value = 0
- exp_mean_over_bp = mean + stddev**2/float(mean+1)
- for (c1,c2) in self.isizes:
- log_likelihood_value += math.log( normpdf(self.isizes[(c1,c2)],exp_mean_over_bp, stddev) ) * self.observations[(c1,c2)][1]
- #for isize in self.isizes[(c1,c2)]:
- # log_likelihood_value += math.log( normpdf(isize,mean,stddev) )
-
- return log_likelihood_value
-
- def calc_dist_objective(self):
- objective_value = 0
- self.get_GapEst_isizes()
- for (c1,c2) in self.isizes:
-
- objective_value += abs(self.gapest_predictions[(c1,c2)] - self.isizes[(c1,c2)]) * self.observations[(c1,c2)][1]
- #for isize in self.isizes[(c1,c2)]:
- # objective_value += math.log( normpdf(isize,mean,stddev) )
-
- return objective_value
-
- def make_path_dict_for_besst(self):
- path_dict = {}
- for ctg1,ctg2 in zip(self.ctgs[:-1],self.ctgs[1:]):
- path_dict[(ctg1,ctg2)] = ctg2.position - (ctg1.position + ctg1.length) - 1
- #print path_dict
- return path_dict
-
-
- def LP_solve_gaps(self):
- exp_means_gapest = {}
- for (i,j) in self.observations:
- mean_obs = self.observations[(i,j)][0]
- exp_means_gapest[(i,j)] = self.observations[(i,j)][0] + GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
- #print mean_obs, self.ctgs[i].length, self.ctgs[j].length, 'gap:' , GC.GapEstimator(self.mean, self.stddev, self.read_len, mean_obs, self.ctgs[i].length, self.ctgs[j].length)
-
-
- #exp_mean_over_bp = self.mean + self.stddev**2/float(self.mean+1)
-
- #calculate individual exp_mean over each edge given observation with gapest??
-
- gap_vars= []
- for i in range(len(self.ctgs)-1):
- gap_vars.append( LpVariable(str(i), None, self.mean + 4*self.stddev, cat='Integer'))
-
- # help variables because objective function is an absolute value
- help_variables = {}
- for (i,j) in self.observations:
- help_variables[(i,j)] = LpVariable("z_"+str(i)+'_'+str(j), None, None,cat='Integer')
-
- # # variables to penalize negative gaps
- # penalize_variables = {}
- # for i in range(len(self.gaps)):
- # penalize_variables[i] = LpVariable("r_"+str(i)+'_'+str(j), None, 0,cat='Integer')
-
- # PENALIZE_CONSTANT = Counter()
- # for (i,j) in self.observations:
- # for k in range(i,j-1): # all gaps between contig i and j
- # # we penalize with the count of all observations spanning over the gap
- # PENALIZE_CONSTANT[k] += self.observations[(i,j)][1] # number of observations spanning over the gap
-
- problem = LpProblem("PathProblem",LpMinimize)
-
- problem += lpSum( [ help_variables[(i,j)]*self.observations[(i,j)][1] for (i,j) in self.observations] ) , "objective"
- # problem += lpSum( [ - penalize_variables[i]*PENALIZE_CONSTANT[i] for i in range(len(self.gaps))] )
-
- # adding constraints induced by the absolute value of objective function
- for (i,j) in self.observations:
- problem += exp_means_gapest[(i,j)] - sum(map(lambda x: x.length, self.ctgs[i+1:j])) - self.observations[(i,j)][0] - lpSum( gap_vars[i:j] ) <= help_variables[(i,j)] , "helpcontraint_"+str(i)+'_'+ str(j)
-
- for (i,j) in self.observations:
- problem += - exp_means_gapest[(i,j)] + lpSum( gap_vars[i:j] ) + sum(map(lambda x: x.length, self.ctgs[i+1:j])) + self.observations[(i,j)][0] <= help_variables[(i,j)] , "helpcontraint_negative_"+str(i)+'_'+ str(j)
-
-
- # adding distance constraints
-
- for (i,j) in self.observations:
- problem += lpSum( gap_vars[i:j] ) + sum(map(lambda x: x.length, self.ctgs[i+1:j])) + self.observations[(i,j)][0] <= self.mean +4*self.stddev , "dist_constraint_"+str(i)+'_'+ str(j)
-
- for (i,j) in self.observations:
- problem += - lpSum( gap_vars[i:j] ) - sum(map(lambda x: x.length, self.ctgs[i+1:j])) - self.observations[(i,j)][0] <= - self.mean +4*self.stddev , "dist_constraint_negative_"+str(i)+'_'+ str(j)
-
- # # Adding constraints induced from introducing a negative gap penalizer
- # for i in range(len(self.gaps)):
- # problem += penalize_variables[i] - gap_vars[i] <= 0 , "neg_gap_contraint_"+str(i)
-
-
- try:
- problem.solve()
- except : #PulpSolverError:
- print 'Could not solve LP, printing instance:'
- print 'Objective:'
- print problem.objective
- print 'Constraints:'
- print problem.constraints
-
- print 'Solving with ordered_search instead'
- path = ordered_search(self)
- return path.gaps
-
- optimal_gap_solution = [0]*(len(self.ctgs) -1)
- for v in problem.variables():
- try:
- optimal_gap_solution[int( v.name)] = v.varValue
- #print v.name, "=", v.varValue
- except ValueError:
- pass
-
- #print optimal_gap_solution
- return optimal_gap_solution
-
- def __str__(self):
- string= ''
- for ctg in self.ctgs:
- string += 'c'+str(ctg.index) +',startpos:'+ str(ctg.position)+',endpos:'+str(ctg.position + ctg.length)+'\n'
-
- return string
-
-
-def MCMC(path, mean,stddev):
-
- path.get_inferred_isizes()
- iteration = 0
- curr_state_count = 1 # how many iterations we have remained in state
- while True:
- # print 'CURRENT PATH:'
- # print path
- # print 'With likelihood: ', path.calc_log_likelihood(mean,stddev)
-
- # change gaps
- # MCMC based sampling:
- # take the most deviant mean insert size observation (x_hat = o_hat + current_gap)
- # given the current positioning.
- # Adjust the current_gap to new_gap so that o_hat + new_gap = mean
-
- suggested_path = path.propose_new_state_MCMC(mean,stddev)
- suggested_path.update_positions()
- suggested_path.get_inferred_isizes()
- suggested_path.calc_log_likelihood(mean,stddev)
-
- # print 'SUGGESTED PATH:'
- # print suggested_path
- # print 'Suggested path likelihood: ', suggested_path.calc_log_likelihood(mean,stddev)
- # compare likelihood values ML value for path
- if suggested_path.calc_log_likelihood(mean,stddev) > path.calc_log_likelihood(mean,stddev):
- #print "SWITCHED PATH TO SUGGESTED PATH!!"
- path = suggested_path
- curr_state_count = 1
- else:
- #print 'PATH not taken!'
- curr_state_count += 1
-
-
-
-
- # see if "converged" or not
- if curr_state_count >= 10:
- break
-
-
- iteration += 1
- if iteration >= 100:
- break
-
- # print 'FINAL PATH:'
- # print path
- # print 'With likelihood: ', path.calc_log_likelihood(mean,stddev)
-
- return path
-
-def ordered_search(path):
-
- path.get_inferred_isizes()
-
- for c1 in range(len(path.ctgs)-1):
- for c2 in range(c1+1,len(path.ctgs)):
- if (c1,c2) in path.observations:
- suggested_path = path.new_state_for_ordered_search(c1,c2,path.mean,path.stddev)
- suggested_path.update_positions()
- suggested_path.get_inferred_isizes()
- suggested_path.calc_dist_objective()
- if suggested_path.calc_dist_objective() < path.calc_dist_objective():
- #print "SWITCHED PATH TO SUGGESTED PATH!!"
- path = suggested_path
- #print path
- else:
- pass
- #print 'PATH not taken!'
- else:
- continue
-
- # print 'FINAL PATH:'
- # print path
- # print 'With likelihood: ', path.calc_log_likelihood(mean,stddev)
-
- return path
-
-def main(contig_lenghts, observations, mean, stddev, read_len):
- """
- contig_lenghts: Ordered list of integers which is contig lengths (ordered as contigs comes in the path)
- observations: dictionary oflist of observations, eg for contigs c1,c2,c3
- we can have [(c1,c2):[23, 33, 21],(c1,c3):[12,14,11],(c2,c3):[11,34,32]]
- """
-
- path = Path(contig_lenghts,observations, mean, stddev, read_len)
-
- # ML_path = MCMC(path,mean,stddev)
- # ML_path = ordered_search(path,mean,stddev)
-
- optimal_LP_gaps = path.LP_solve_gaps()
- path.gaps = optimal_LP_gaps
- path.update_positions()
-
- # print 'MCMC path:'
- # print ML_path
- # print 'MCMC path likelihood:',ML_path.calc_log_likelihood(mean,stddev)
- # print 'Ordered search path:'
- # print ML_path
- # print 'Ordered search likelihood:',ML_path.calc_log_likelihood(mean,stddev)
- # return ML_path
-
- return path
-
-if __name__ == '__main__':
- contig_lenghts = [3000,500,500,500,3000]
- observations_normal = {(0,1):[1800,2000], (0,2):[1500,1800,1400,1700], (0,3):[1200,800,1000],
- (1,2):[750,800],(1,3):[600,700], (1,4):[300,600,700],
- (2,3):[700,750], (2,4):[1400,1570],
- (3,4):[2000,1750], }
-
- observations_linear = {(0,1):[450,500], (1,2):[750,800],
- (2,3):[700,750], (3,4):[400,170]}
-
- # The imortance of support:
- # one edge with a lot of observatins contradicting the others
- observations_matter = {(0,1):[450,500], (1,2):[750,800],
- (2,3):[700,750], (3,4):[400,170],
- (0,4):[700]*30 }
-
- # long contig, 500bp gap, 3*short_contigs, long contig
- observations = {(0,1):[1450,1300,1200,1570], (0,2):[700,800,1000], (0,3):[250,300],
- (1,2):[900],(1,3):[900,800], (1,4):[800,900,1000],
- (2,3):[900], (2,4):[900,800],
- (3,4):[1500,1750,1350,1900,1950] }
-
- # negative gaps test case here:
-
-
- mean = 1500
- stddev = 500
- read_len = 100
- main(contig_lenghts,observations,mean,stddev, read_len)
-
-
diff --git a/external/gatb-minia-pipeline/BESST/BESST/plots.py b/external/gatb-minia-pipeline/BESST/BESST/plots.py
deleted file mode 100644
index 92ecd6a2e07965c7b7ead89f0c2cdea96f3cead3..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/plots.py
+++ /dev/null
@@ -1,88 +0,0 @@
-'''
-Created on Aug 12, 2013
-
-@author: ksahlin
-'''
-
-import os
-
-try:
- import matplotlib
- matplotlib.use('Agg')
- import matplotlib.pyplot as plt
-except ImportError, RuntimeError:
- pass
-
-
-def histogram(x_, param, bins=20, x_label='x', y_label='y', title='Histogram',nr_obs = 10000):
- x = x_[:nr_obs] # If many contigs/edges we only plot 10 000 (default) for time and visuability purposes
- dest = os.path.join(param.output_directory, 'plots', title + '.png')
- plt.hist(x, bins)
- plt.xlabel(x_label)
- plt.ylabel(y_label)
- plt.title(title)
-
- plt.savefig(dest)
- plt.clf()
- return()
-
-def dot_plot(x_, y_, param, x_label='x', y_label='y', title='Dotplot', set_marker='o'):
- x = x_[:10000] # If many contigs/edges we only plot 10 000 for time and visuability purposes
- y = y_[:10000] # If many contigs/edges we only plot 10 000 for time and visuability purposes
- dest = os.path.join(param.output_directory, 'plots', title + '.png')
- plt.scatter(x, y, marker=set_marker)
- plt.xlabel(x_label)
- plt.ylabel(y_label)
- plt.title(title)
- plt.grid(True)
-
- plt.savefig(dest)
- plt.clf()
- return
-
-
-def multiple_histogram(list_of_datasets_, param, x_label='x', y_label='y', title='Stacked_histogram'):
- list_of_datasets = [list[:10000] for list in list_of_datasets_]
- dest = os.path.join(param.output_directory, 'plots', title + '.png')
- # filter out if any of the lists contains 0 elemnets
- list_of_datasets = filter(lambda x: len(x) > 0, list_of_datasets)
- for dataset in list_of_datasets:
- plt.hist(dataset, alpha=0.5)
- plt.xlabel(x_label)
- plt.ylabel(y_label)
- plt.title(title)
-
- plt.savefig(dest)
- plt.clf()
-
- return()
-
-
-
-
-
-#def VizualizeGraph(G, param, Information):
-# import os
-# try:
-# import matplotlib
-# matplotlib.use('Agg')
-#
-# try:
-# os.mkdir(param.output_directory + '/graph_regions' + str(int(param.mean_ins_size)))
-# except OSError:
-# #directory is already created
-# pass
-# counter = 1
-# import copy
-#
-# G_copy = copy.deepcopy(G)
-# RemoveIsolatedContigs(G_copy, Information)
-# CB = nx.connected_component_subgraphs(G_copy)
-# for cycle in CB:
-# nx.draw(cycle)
-# matplotlib.pyplot.savefig(param.output_directory + 'graph_regions' + str(int(param.mean_ins_size)) + '/' + str(counter) + '.png')
-# matplotlib.pyplot.clf()
-# counter += 1
-# except ImportError:
-# pass
-# return()
diff --git a/external/gatb-minia-pipeline/BESST/BESST/worker.py b/external/gatb-minia-pipeline/BESST/BESST/worker.py
deleted file mode 100644
index 83f9aaa57f6f664d4e3453e4638866162c67b3cf..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/worker.py
+++ /dev/null
@@ -1,156 +0,0 @@
-'''
- Created on Oct 30, 2012
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-
-import multiprocessing, Queue
-import ExtendLargeScaffolds as ELS
-class Worker(multiprocessing.Process):
-
- def __init__(self, work_queue, result_queue):
-
- # base class initialization
- multiprocessing.Process.__init__(self)
-
- # job management stuff
- self.work_queue = work_queue
- self.result_queue = result_queue
- self.kill_received = False
- def run(self):
- while not self.kill_received:
-
- # get a task
- #job = self.work_queue.get_nowait()
- worker_name = multiprocessing.current_process().name
- try:
- jobs, G, G_prime, small_scaffolds, end = self.work_queue.get_nowait()
- except Queue.Empty:
- break
-
- # the actual processing
- all_paths_sorted_wrt_score = ELS.BetweenScaffolds(G, G_prime, small_scaffolds, end, jobs)
- self.result_queue.put(all_paths_sorted_wrt_score)
- print 'Exited from ', worker_name
-
- #return()
-
-# for job in jobs:
-# start_node = job[0]
-# end_node = job[1]
-# #nr_paths = find_all_paths(graph, start_node, end_node)
-# #print nr_paths, multiprocessing.current_process().name
-# # store the result
-# self.result_queue.put(nr_paths)
-#import os
-
- #result_queue.put(all_paths_sorted_wrt_score)
-
- #os.kill()
-
-result_list = []
-def log_result(result):
- # This is called whenever foo_pool(i) returns a result.
- # result_list is modified only by the main process, not the pool workers.
- print 'Going in here'
- result_list.append(result)
-def worker(jobs, G, G_prime, small_scaffolds, end):
- worker_name = multiprocessing.current_process().name
- # the actual processing
- all_paths_sorted_wrt_score = ELS.BetweenScaffolds(G, G_prime, small_scaffolds, end, jobs)
- print 'Exited from ', worker_name
- return(all_paths_sorted_wrt_score)
-
-def BetweenScaffoldsParallellized(G, G_prime, small_scaffolds, num_processes, end):
- import multiprocessing , Queue
- #import worker #(multi processing)
- import heapq
-
- #import random
-# end = set()
-# for node in G:
-# end.add(node)
-
- # load up work queue
- work_queue = multiprocessing.Queue()
- nodes = G.nodes()
- #random.shuffle(nodes)
- nr_jobs = len(nodes)
- chunk = nr_jobs / num_processes
- #print jobs, nr_jobs, chunk
- counter = 0
-
- # partition equally many nodes in G to each core
- while counter < nr_jobs:
- work_queue.put((set(nodes[counter:counter + chunk]), G, G_prime, small_scaffolds, end))
- print 'node nr', counter, 'to', counter + chunk - 1, 'added'
- counter += chunk
-
- # create a queue to pass to workers to store the results
- #result_queue = multiprocessing.Queue()
-
- pool = multiprocessing.Pool()
- #num_processes = multiprocessing.cpu_count()
- #for i in range(0,num_processes):
- while not work_queue.empty():
- nodes, G, G_prime, small_scaffolds, end = work_queue.get_nowait()
- pool.apply_async(worker, args=(nodes, G, G_prime, small_scaffolds, end), callback=log_result)
- pool.close()
- pool.join()
- #print(result_list)
-
-#
-# jobs = []
-# for i in range(num_processes):
-# try:
-# nodes, G, G_prime, small_scaffolds, end = work_queue.get_nowait()
-# print 'Time to work'
-# except Queue.Empty:
-# print 'lol no work'
-# p = multiprocessing.Process(target=worker.worker, args=(nodes, G, G_prime, small_scaffolds, end,result_queue))
-# jobs.append(p)
-# print 'job nr ',i, 'start'
-# p.start()
-
-#
-# # spawn workers (equally many as available cores)
-# workers =[]
-# for i in range(0,num_processes):
-# workers.append(MP.Worker(work_queue, result_queue))
-# workers[i].start()
- #print 'hejhej!'
- work_queue.close() # Indicate that no more data will be put on this queue by the current process
- # Wait for the workers to finish
-# for i in range(0,num_processes):
-# jobs[i].join()
-# print "I'm waiting..."
-# #workers[i].join()
-
- # collect the results off the queue
- def wrapper(func, args):
- return(func(*args))
- #tot_result = []
-
- #while not result_queue.empty():
- # tot_result.append(result_queue.get())
- #print 'tot result', tot_result
- #Merge the scored paths from each of the subprocesses into one consensus path
- itr = wrapper(heapq.merge, result_list) #tot_result)
-
- return(itr)
diff --git a/external/gatb-minia-pipeline/BESST/BESST/workerprocess.py b/external/gatb-minia-pipeline/BESST/BESST/workerprocess.py
deleted file mode 100644
index 5244188e1c486b2e2c5f46556c8c9b9d0ae79aab..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/BESST/workerprocess.py
+++ /dev/null
@@ -1,70 +0,0 @@
-'''
- Created on Jun 17, 2012
-
- @author: ksahlin
-
- This file is part of BESST.
-
- BESST is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- BESST is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with BESST. If not, see <http://www.gnu.org/licenses/>.
- '''
-
-
-import networkx as nx
-from itertools import combinations
-import random
-import multiprocessing , Queue
-import time
-import ExtendLargeScaffolds as ELS
-
-
-class Worker(multiprocessing.Process):
-
- def __init__(self, work_queue, result_queue):
-
- # base class initialization
- multiprocessing.Process.__init__(self)
-
- # job management stuff
- self.work_queue = work_queue
- self.result_queue = result_queue
- self.kill_received = False
- def run(self):
- #while not self.kill_received:
-
- # get a task
- #job = self.work_queue.get_nowait()
- #try:
- job = self.work_queue #.get_nowait()
- start_nodes = job[0]
- G_prime = job[1]
- #small_scaffolds = job[2]
- end = job[2]
- param = job[3]
- #all_paths_sorted_wrt_score = [(1,[]),(2,[])]
-
- # except Queue.Empty:
- # print 'Noeee! empty!!', multiprocessing.current_process().name
- # break
-
- print 'Enter ', multiprocessing.current_process().name
- # the actual processing
- all_paths_sorted_wrt_score = ELS.BetweenScaffolds(G_prime, end, start_nodes, param)
- #all_paths_sorted_wrt_score = [(1,[]),(2,[])]
- #nr_paths = find_all_paths(graph, start_node, end_node)
- # store the result
- self.result_queue.put(all_paths_sorted_wrt_score)
- print 'Exit', multiprocessing.current_process().name
-
-
-
diff --git a/external/gatb-minia-pipeline/BESST/LICENSE.txt b/external/gatb-minia-pipeline/BESST/LICENSE.txt
deleted file mode 100644
index 8c73349ec9d0839bb5628889074d372b53f1f693..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/LICENSE.txt
+++ /dev/null
@@ -1,15 +0,0 @@
- BESST - Scaffolder for genomic assemblies
- Copyright (C) 2013 Kristoffer Sahlin
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
diff --git a/external/gatb-minia-pipeline/BESST/README.md b/external/gatb-minia-pipeline/BESST/README.md
deleted file mode 100644
index f07ab5863646a40fb75bdee1c83ab82f63321746..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/README.md
+++ /dev/null
@@ -1,221 +0,0 @@
-BESST
-========
-
-BESST is a package for scaffolding genomic assemblies. It contains several modules for e.g. building a "contig graph" from available information, obtaining scaffolds from this graph, and accurate gap size information (based on GapEst [1]). BESST is first described in [2] and a paper describing later improvements is forthcoming.
-
-For installation, see docs/INSTALL.md. Manual is found in docs/MANUAL.md.
-
-Please cite [2] and later manuscripts when using BESST! BiBTeX entries are available in the file besst.bib.
-
-1. Sahlin K, Street N, Lundeberg J, Arvestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222 [Link](http://bioinformatics.oxfordjournals.org/content/28/17/2215.long)
-2. Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281 [Link](http://www.biomedcentral.com/1471-2105/15/281)
-
-
-INSTALLATION
-----------------
-See docs/INSTALL.md.
-
-Q&A
-------------------
-
-#### What parameters should I call BESST with?
-BESST is designed to infer as much as possible from data. If this is your first time running BESST, it is highly reccomended to run BESST with as few parameters set as possible, i.e.,
-
-```sh
-runBESST -c /path/to/contigfile.fa -f /path/to/file1.bam /path/to/file2.bam ... -o /path/to/output --orientation {fr/rf}
-```
-For more details, see section "INPUT" further down. BESST will then infer as much as possible from data and print inferred parameters and more to "/path/to/output/BESST_output/Statistics.txt". This file is useful for debugging.
-
-#### What aligner should I use?
-BESST requires only a sorted and indexed BAM file -- your favourite aligner can be used. However, we have had the best experience with BWA-mem using default parameters on most data used in our evaluations.
-
-#### What aligner options are good/bad?
-BESST only work with uniquely aligned reads for now (with the aim to extend it to consider probability distribution over multiple alignments). The uniqueness is detected in the sorted BAM file by looking at the flag. Therefore, it is NOT suitable to specify any parameter that makes the aligner output several (suboptimal) alignments of a read, and reporting the read as mapped to multiple locations. Bowtie's "-k <int>" (with int other than 1) is an example of a parameter that is not compatible with BESST.
-
-#### My mate pair libraries contains paired-end contamination, what should I do?
-
-First off, always use an adaptertrimming tool. The trimming of adapters greatly improves alignments as both adapters, and chimeric parts withing reads (result of read sequence on different sides of the adapter), can greatly improve alignments and therefore scaffolding. We recommend any tool that can separate the paired reads types into MP, PE, and unknown orientation based on identifying and <em>removing</em> the adapters (we have had good experience with the tool NxTrim)
-
-###### Few adapters found -> read pairs have unknown orientation
-In case the you cannot single out any (or only a small fraction) of mate pairs based on adapter finding, just run BESST as default. BESST identifies MP distribution, PE contamination level and distribution by alignemtns on contigs. Do not specify -m and -s in this case as BESST has a relatively advanced inference of library characteristics (some of it from theory described in [GetDistr](http://biorxiv.org/content/biorxiv/early/2015/08/04/023929.full.pdf) ).
-
-###### Significant amount of adapters found
-From the MP libraries we have worked with, we usually see around 30% of each of the three categories MP, PE, and unknown and should be relatively normal (see contamination levels investigation in supplemental data in [NxTrim](http://bioinformatics.oxfordjournals.org/content/early/2015/02/05/bioinformatics.btv057/suppl/DC1)). In case you can single out approximately this amount of MPs and PEs: The paired end contamination can still help BESST scaffolding by providing short range links complimentaty to long range MP links. The usage of these information sources simultaneosly as partly described in [BESST-v2](http://www.biorxiv.org/content/early/2015/08/28/025650.abstract) improves scaffolding over a stepwise approach that BESST and other stand-alone scaffolders takes in case of several separated libraries. We recommend to use the full <em>adapter trimmed</em> library i.e., all MP, PE, and unknown reads together, with original orientations preserved, in case the distributions on the PE and MP are distinctively separated and the assembly contains enough small contigs where the short-range PE can help (say N75 < mean of MP as an approximation). See figure for an example of a clearly separated MP distribution. Notice that e.g. NxTrim will output all reads in fr orientation so the MPs will have to be reverse complemented back.
-
-
-
-In case the MP distribution is wide and already has good short-range spanning coverge and good coverage in general, use only the links that were identified as MPs. Below is an example of such a distribution
-
-
-
-
-The safe approach is of course always to try both.
-
-
-#### BESST does not scaffold anything, what is going on?
-
-A lot of debugging can be done immediately in "< outputfolder >/BESST_output/Statistics.txt" file where outputfolder is specified with -o when running BESST. BESST outputs statistics of insert size distribution(s) (mate-pair and PE-contamination) as well as coverage statistics and how many read pair are used for scaffolding (for each library). Below is an example of the beginning of a file. Make sure library distribution, contamine distribution and rate looks ok, as well as coverage statistics. If this does not resolve issues or you are unsure about how to proceed, please mail **ksahlin@kth.se**.
-
-```sh
-PASS 1
-
-
-Mean before filtering : 2471.05005763
-Std_est before filtering: 1621.22128565
-Mean converged: 2454.01278202
-Std_est converged: 1438.84572664
-Contamine mean before filtering : 383.841809945
-Contamine stddev before filtering: 541.063248334
-Contamine mean converged: 371.132937665
-Contamine std_est converged: 105.713828422
-
-LIBRARY STATISTICS
-Mean of library set to: 2454.01278202
-Standard deviation of library set to: 1438.84572664
-MP library PE contamination:
-Contamine rate (rev comp oriented) estimated to: 0.228445050646
-lib contamine mean (avg fragmentation size): 371.132937665
-lib contamine stddev: 105.713828422
-Number of contamined reads used for this calculation: 106857.0
--T (library insert size threshold) set to: 8209.39568857
--k set to (Scaffolding with contigs larger than): 8209.39568857
-Number of links required to create an edge: 5
-Read length set to: 100.38
-Relative weight of dominating link set to (default=3): 3
-
-Time elapsed for getting libmetrics, iteration 0: 41.3993628025
-
-Parsing BAM file...
-L50: 37 N50: 42455 Initial contig assembly length: 4588376
-Nr of contigs that was singeled out due to length constraints 78
-Time initializing BESST objects: 0.00225305557251
-Nr of contigs/scaffolds included in scaffolding: 130
-Total time elapsed for initializing Graph: 0.00791215896606
-Reading bam file and creating scaffold graph...
-ELAPSED reading file: 30.2451779842
-NR OF FISHY READ LINKS: 0
-Number of USEFUL READS (reads mapping to different contigs uniquly): 434284
-Number of non unique reads (at least one read non-unique in read pair) that maps to different contigs (filtered out from scaffolding): 29267
-Reads with too large insert size from "USEFUL READS" (filtered out): 325897
-Number of duplicated reads indicated and removed: 4890
-Mean coverage before filtering out extreme observations = 69.01403104
-Std dev of coverage before filtering out extreme observations= 61.5185426061
-Mean coverage after filtering = 51.1057077906
-Std coverage after filtering = 17.4310506587
-Length of longest contig in calc of coverage: 106467
-Length of shortest contig in calc of coverage: 8270
-```
-
-
-
-NOTE:
-----
-#### Common pitfall: ####
-
-If `--orientation` is not specified, BESST assumes that all libraries was aligned in fr orientation.
-(In versions less than 1.2 BESST cannot parse rf orientations. Thus, BESST requires reads to be mapped in FR mode, i.e. `---> <---`, matepairs thus need to be reverse complemented.)
-
-
-#### Time and memory requirements: ####
-Version 1.3 and later have implemented several major improvements in runtime and memory requirements. These fixes has the most effect on large fragmented assemblies with hundereds of thousands to millions of contigs.
-
-#### BAM files and mapping ####
-BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in paired read mode. BESST provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is
-
-```sh
-python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_A.fq /path/to/contigs.fasta --threads N
-```
-where `N` is an integer specifying how many threads BWA-mem should use. `--nomem` can be specified to the above call to use BWA-sampe as the paired read alignment pipeline.
-
-INPUT:
-------
-Required arguments:
-
-* -c < path to a contig file >
-
-* -f < path to BAM files > (increasing order of insert size)
-
-* -o < path to location for the output >
-
-Highly recommended argument:
-
-* --orientation < fr/rf one for each library >
-
-EXAMPLE RUN:
------------
-For scaffolding with one PE and one MP library:
-```sh
-runBESST -c /path/to/contigfile.fa -f /path/to/file1.bam /path/to/file2.bam -o /path/to/output --orientation fr rf
-```
-If the mate pair library was reversed complemented before it was aligned, '--orientation fr fr' should be specified.
-
-Optional arguments:
--------------------
-
-The following arguments are computed internally / set by BESST. It is however good to specify mean and standard deviation if your assembly is very fragmented compared to the library insert size (not enough large contains to compute library statistics on).
-
-#### Library parameters: ####
-
-* -m <int> : the means of the insert sizes of the library, one integer number for each library.
-
-* -s <int> : standard deviation of the libraries, one integer number for each library.
-
-* -T <int> : Thresholds that are some upper levels that you think not too many PE/MP will have a longer insert size than (in the end of the mode).
-
-* -r <int> : Mean read length for each of the libraries.
-
-* -z <int ... > Coverage cutoff for repeat classification ( e.g. -z 100 says that contigs with coverages over 100 will be discarded from scaffolding). One cutoff for each library.
-
-* -d Check for sequencing duplicates and count only one of them (when computing nr of links) if they are occurring.
-
-#### Contig parameters: ####
-
-* -k <ints> Minimum contig size to be seen as a "large contigs" (for statistical scoring only). One number for each library.
-
-* --filter_contigs <int> Remove contigs smaller than this value from all scaffolding. These contigs are not even incuded in the outpus of BESST.
-
-
-#### Algorithm parameters: ####
-
-* --iter <int> Maximum number of iterations in BFS search for paths between scaffolds.
-
-* --max_extensions <int> Maximum number of extensions performed between contig/scaffold ends.
-
-* -e <int> The least amount of witness links that is needed to create a link edge in graph (one for each library)
-
-* -y Extend scaffolds with smaller contigs (default on).
-
-* --no_score Do not perform statistical scoring, only run path search between contigs.
-
-* --score_cutoff <float> Only consider paths with score > score_cutoff (default 1.5)
-
-
-
-#### Under construction / proven unstable ####
-
-* -g [0/1] Haplotype detection function on or off. (default = 0 (off) <0 or 1>)
-
-* -a <float> Maximum length difference ratio for merging of haplotypic regions.
-
-* -b <int> Nr of standard deviations over mean/2 of coverage to allow for clasification of haplotype
-
-* -q Parallellize work load of path finder module in case of multiple processors available using multiprocessing library for pyhton.
-
-
-MORE NOTES:
--------
-
-1. Definition of insert size: BESST assumes the following definitions:
- * insert size = fragment length.
- * For PE:
- ```
- s t
- ------> <-------
- ```
- from s to t, that is, insertsize = readlen1 + gap + readlen2. So when mean and/or threshold is supplied, it should be mean and threshold of this distance.
-
-2. Mapping reads: If you want to map a mate pair library, you will need to map them as paired end library i.e. forward-reverse mode. All read pair libraries should be in this order.
-
-3. Order of scaffolding: It is crucial for the algorithm that you give the libraries in increasing order of the insert size.
-
-
diff --git a/external/gatb-minia-pipeline/BESST/besst.bib b/external/gatb-minia-pipeline/BESST/besst.bib
deleted file mode 100644
index 1eb861d6db8df4069a122161e8b67cb3827c0c35..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/besst.bib
+++ /dev/null
@@ -1,70 +0,0 @@
-@article{Sahlin2014,
- author = {Sahlin, K. and Vezzi, F. and Nystedt, B. and Lundeberg, J. and Arvestad, L.},
- title = {{BESST}--efficient scaffolding of large fragmented assemblies.},
- journal = {BMC Bioinformatics},
- volume = {15},
- year = {2014},
- pages = {281},
- pmid = {25128196},
- doi = {10.1186/1471-2105-15-281},
- abstract = {BACKGROUND: The use of short reads from High Throughput Sequencing
-(HTS) techniques is now commonplace in de novo assembly. Yet,
-obtaining contiguous assemblies from short reads is challenging,
-thus making scaffolding an important step in the assembly pipeline.
-Different algorithms have been proposed but many of them use the
-number of read pairs supporting a linking of two contigs as an
-indicator of reliability. This reasoning is intuitive, but fails
-to account for variation in link count due to contig features.We
-have also noted that published scaffolders are only evaluated
-on small datasets using output from only one assembler. Two issues
-arise from this. Firstly, some of the available tools are not
-well suited for complex genomes. Secondly, these evaluations provide
-little support for inferring a software's general performance.
-RESULTS: We propose a new algorithm, implemented in a tool called
-BESST, which can scaffold genomes of all sizes and complexities
-and was used to scaffold the genome of P. abies (20 Gbp). We
-performed a comprehensive comparison of BESST against the most
-popular stand-alone scaffolders on a large variety of datasets.
-Our results confirm that some of the popular scaffolders are
-not practical to run on complex datasets. Furthermore, no single
-stand-alone scaffolder outperforms the others on all datasets.
-However, BESST fares favorably to the other tested scaffolders
-on GAGE datasets and, moreover, outperforms the other methods
-when library insert size distribution is wide. CONCLUSION: We
-conclude from our results that information sources other than
-the quantity of links, as is commonly used, can provide useful
-information about genome structure when scaffolding.}
-}
-@article{Sahlin2012,
- author = {Sahlin, K. and Street, N. and Lundeberg, J. and Arvestad, L.},
- title = {Improved gap size estimation for scaffolding algorithms.},
- journal = {Bioinformatics},
- volume = {28},
- number = {17},
- year = {2012},
- month = {Sep},
- pages = {2215-2222},
- pmid = {22923455},
- doi = {10.1093/bioinformatics/bts441},
- abstract = {MOTIVATION: One of the important steps of genome assembly is scaffolding,
-in which contigs are linked using information from read-pairs.
-Scaffolding provides estimates about the order, relative orientation
-and distance between contigs. We have found that contig distance
-estimates are generally strongly biased and based on false assumptions.
-Since erroneous distance estimates can mislead in subsequent analysis,
-it is important to provide unbiased estimation of contig distance.
-RESULTS: In this article, we show that state-of-the-art programs
-for scaffolding are using an incorrect model of gap size estimation.
-We discuss why current maximum likelihood estimators are biased
-and describe what different cases of bias we are facing. Furthermore,
-we provide a model for the distribution of reads that span a gap
-and derive the maximum likelihood equation for the gap length.
-We motivate why this estimate is sound and show empirically that
-it outperforms gap estimators in popular scaffolding programs.
-Our results have consequences both for scaffolding software, structural
-variation detection and for library insert-size estimation as
-is commonly performed by read aligners. AVAILABILITY: A reference
-implementation is provided at \verb+https://github.com/SciLifeLab/gapest.+
-SUPPLEMENTARY INFORMATION: Supplementary data are availible at
-Bioinformatics online.}
-}
diff --git a/external/gatb-minia-pipeline/BESST/docs/INSTALL.md b/external/gatb-minia-pipeline/BESST/docs/INSTALL.md
deleted file mode 100644
index b56c17f057ff613bd0521ed493892d68f2fa3e3a..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/docs/INSTALL.md
+++ /dev/null
@@ -1,57 +0,0 @@
-INSTALLATION:
---------------
-
-Below gives three options to install BESST.
-
-Source from GitHub
------------------
-This assumes that you have the python modules pysam, networkx, numpy and scipy installed.
-
-```sh
-git clone https://github.com/ksahlin/BESST.git
-cd BESST
-./runBESST
-```
-
-
-Using pip or easy_install (recommended)
----------------------------------------------------
-Python has two package installers, *pip* and *easy_install*, which makes it very easy to install **BESST**. If you have any of this installed,
-
-Type for *pip* (in terminal):
-```
-sudo pip install BESST
-```
-Type for *easy_install* (in terminal):
-```
-sudo easy_install BESST
-```
-If you do not have *pip* or *easy_install* for python, you can get e.g. *pip* as follows:
-```
-curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
-python get-pip.py
-```
-With proper installation of **BESST**, you should be able to run:
-
-```
-runBESST
-```
-
-to view user instructions.
-
-(This installation will install the two nonstandard python module dependencies: *pysam 0.6*, *networkx-1.6* automatically for you.)
-
-
-
-Installing manually
--------------------
-
-In the **BESST** folder where *setup.py* is located, run:
-
-```python setup.py install```
-
-This installation will not include the two modules *networkx* and *pysam*. You need to install them separately. They can be found here:
-
-http://networkx.github.com/documentation/latest/install.html
-
-http://code.google.com/p/pysam/downloads/list
diff --git a/external/gatb-minia-pipeline/BESST/docs/MANUAL.md b/external/gatb-minia-pipeline/BESST/docs/MANUAL.md
deleted file mode 100644
index 473b58c1362f5cc82e32d70e8a7decc7089a8073..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/docs/MANUAL.md
+++ /dev/null
@@ -1,211 +0,0 @@
-BESST
-======
-
-INSTALLATION
-----------------
-See docs/INSTALL.md.
-
-Q&A
-------------------
-
-#### What parameters should I call BESST with?
-BESST is designed to infer as much as possible from data. If this is your first time running BESST, it is highly reccomended to run BESST with as few parameters set as possible, i.e.,
-
-```sh
-runBESST -c /path/to/contigfile.fa -f /path/to/file1.bam /path/to/file2.bam ... -o /path/to/output --orientation {fr/rf}
-```
-For more details, see section "INPUT" further down. BESST will then infer as much as possible from data and print inferred parameters and more to "/path/to/output/BESST_output/Statistics.txt". This file is useful for debugging.
-
-#### What aligner should I use?
-BESST requires only a sorted and indexed bamfile -- your favourite aligner can be used. However, we have had the best experience with BWA-mem using default parameters on most data used in our evaluations.
-
-#### What aligner options are good/bad?
-BESST only work with uniquely aligned reads for now (with the aim to extend it to consider probability distribution over multiple alignments). The uniqueness is detected in the sorted BAM file by looking at the flag. Therefore, it is NOT suitable to specify any parameter that makes the aligner output several (suboptimal) alignments of a read, and reporting the read as mapped to multiple locations. Bowtie's "-k <int>" (with int other than 1) is an example of a parameter that is not compatible with BESST.
-
-#### My mate pair libraries contains paired-end contamination, what should I do?
-
-First off, always use an adaptertrimming tool. The trimming of adapters greatly improves alignemtns as both adapters, and chimeric parts withing reads (result of read sequence on different sides of the adapter), can greatly improve alignments and therefore scaffolding. We recommend any tool that can separate the paired reads types into MP, PE and unknown orientation based on identifying and <em>removing</em> the adapters (we have had good experience with the tool NxTrim)
-
-###### Few adapters found -> read pairs have unknown orientation
-In case the you cannot single out any (or only a small fraction) of mate pairs based on adapter finding, just run BESST as default. BESST identifies MP distribution, PE contamination level and distribution by alignemtns on contigs. Do not specify -m and -s in this case as BESST has a relatively advanced inference of library characteristics (some of it from theory described in [GetDistr](http://biorxiv.org/content/biorxiv/early/2015/08/04/023929.full.pdf) ).
-
-###### Significant amount of adapters found
-From the MP libraries we have worked with, we usually see around 30% of each of the three categories MP,PE and unknown and should be relatively normal (see contamination levels investigation in supplemental data in [NxTrim](http://bioinformatics.oxfordjournals.org/content/early/2015/02/05/bioinformatics.btv057/suppl/DC1)). In case you can single out approximately this amount of MPs and PEs: The paired end contamination can still help BESST scaffolding by providing short range links complimentaty to long range MP links. The usage of these information sources simultaneosly as partly described in [BESST-v2](http://www.biorxiv.org/content/early/2015/08/28/025650.abstract) improves scaffolding over a stepwise approach that BESST and other stand-alone scaffolders takes in case of several separated libraries. We recommend to use the full <em>adapter trimmed</em> library i.e., all MP, PE and unknown reads together, with original orientations preserved, in case the distributions on the PE and MP are distinctively separated and the assembly contains enough small contigs where the short-range PE can help (say N75 < mean of MP as an approximation). See figure for an example of a clearly separated MP distribution. Notice that e.g. NxTrim will output all reads in fr orientation so the MPs will have to be reverse complemented back.
-
-
-
-In case the MP distribution is wide and already has good short-range spanning coverge and good coverage in general, use only the links that were identified as MPs. Below is an example of such a distribution
-
-
-
-
-The safe approach is of course always to try both.
-
-
-#### BESST does not scaffold anything, what is going on?
-
-A lot of debugging can be done immediately in "< outputfolder >/BESST_output/Statistics.txt" file where outputfolder is specified with -o when running BESST. BESST outputs statistics of insert size distribution(s) (mate-pair and PE-contamination) as well as coverage statistics and how many read pair are used for scaffolding (for each library). Below is an example of the beginning of a file. Make sure library distribution, contamine distribution and rate looks ok, as well as coverage statistics. If this does not resolve issues or you are unsure about how to proceed, please mail **ksahlin@kth.se**.
-
-```sh
-PASS 1
-
-
-Mean before filtering : 2471.05005763
-Std_est before filtering: 1621.22128565
-Mean converged: 2454.01278202
-Std_est converged: 1438.84572664
-Contamine mean before filtering : 383.841809945
-Contamine stddev before filtering: 541.063248334
-Contamine mean converged: 371.132937665
-Contamine std_est converged: 105.713828422
-
-LIBRARY STATISTICS
-Mean of library set to: 2454.01278202
-Standard deviation of library set to: 1438.84572664
-MP library PE contamination:
-Contamine rate (rev comp oriented) estimated to: 0.228445050646
-lib contamine mean (avg fragmentation size): 371.132937665
-lib contamine stddev: 105.713828422
-Number of contamined reads used for this calculation: 106857.0
--T (library insert size threshold) set to: 8209.39568857
--k set to (Scaffolding with contigs larger than): 8209.39568857
-Number of links required to create an edge: 5
-Read length set to: 100.38
-Relative weight of dominating link set to (default=3): 3
-
-Time elapsed for getting libmetrics, iteration 0: 41.3993628025
-
-Parsing BAM file...
-L50: 37 N50: 42455 Initial contig assembly length: 4588376
-Nr of contigs that was singeled out due to length constraints 78
-Time initializing BESST objects: 0.00225305557251
-Nr of contigs/scaffolds included in scaffolding: 130
-Total time elapsed for initializing Graph: 0.00791215896606
-Reading bam file and creating scaffold graph...
-ELAPSED reading file: 30.2451779842
-NR OF FISHY READ LINKS: 0
-Number of USEFUL READS (reads mapping to different contigs uniquly): 434284
-Number of non unique reads (at least one read non-unique in read pair) that maps to different contigs (filtered out from scaffolding): 29267
-Reads with too large insert size from "USEFUL READS" (filtered out): 325897
-Number of duplicated reads indicated and removed: 4890
-Mean coverage before filtering out extreme observations = 69.01403104
-Std dev of coverage before filtering out extreme observations= 61.5185426061
-Mean coverage after filtering = 51.1057077906
-Std coverage after filtering = 17.4310506587
-Length of longest contig in calc of coverage: 106467
-Length of shortest contig in calc of coverage: 8270
-```
-
-
-
-NOTE:
-----
-#### Common pitfall: ####
-
-If --orientation is not specified, BESST assumes that all libraries was aligned in fr orientation.
-(In versions less than 1.2 BESST cannot parse rf orientations. Thus, BESST requires reads to be mapped in FR mode, i.e. ---> <---, matepairs thus need to be reverse complemented.)
-
-
-#### Time and memory requirements: ####
-Version 1.3 and later have implemented several major improvements in runtime and memory requirements. These fixes has the most effect on large fragmented assemblies with hundereds of thousands to millions of contigs.
-
-#### Bam files and mapping ####
-BESST requires sorted and indexed bamfiles as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be aligned in paired read mode. BESST provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py) for obtaining sorted and indexed bamfiles with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is
-
-```sh
-python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_A.fq /path/to/contigs.fasta --threads N
-```
-where N is an integer specifying how many threads BWA-mem should use. --nomem can be specified to the above call to use BWA-sampe as the paired read alignment pipeline.
-
-INPUT:
-------
-Required arguments:
-
-* -c < path to a contig file >
-
-* -f < path to bamfiles > (increasing order of insert size)
-
-* -o < path to location for the output >
-
-Highly recommended argument:
-
-* --orientation < fr/rf one for each library >
-
-EXAMPLE RUN:
------------
-For scaffolding with one PE and one MP library:
-```sh
-runBESST -c /path/to/contigfile.fa -f /path/to/file1.bam /path/to/file2.bam -o /path/to/output --orientation fr rf
-```
-If the mate pair library was reversed complemented before it was aligned, '--orientation fr fr' should be specified.
-
-Optional arguments:
--------------------
-
-The following arguments are computed internally / set by BESST. It is however good to specify mean and standard deviation if your assembly is very fragmented compared to the library insert size (not enough large contains to compute library statistics on).
-
-#### Library parameters: ####
-
-* -m < the means of the insert sizes of the library, one integer number for each library > (integer numbers)
-
-* -s < standard deviation of the libraries, one integer number for each library> (integer numbers)
-
-* -T < Thresholds that are some upper levels that you think not too many PE/MP will have a longer insert size than (in the end of the mode) > (integer numbers)
-
-* -r < Mean read length for each of the libraries > (integer number)
-
-* -z <ints> Coverage cutoff for repeat classification ( e.g. -z 100 says that contigs with coverages over 100 will be discarded from scaffolding). Integer numbers, one for each library)
-
-* -d Check for sequencing duplicates and count only one of them (when computing nr of links) if they are occurring.
-
-#### Contig parameters: ####
-
-* -k <ints> Minimum contig size to be seen as a "large contigs" (for statistical scoring only). One number for each library.
-
-* --filter_contigs <int> Remove contigs smaller than this value from all scaffolding. These contigs are not even incuded in the outpus of BESST.
-
-
-#### Algorithm parameters: ####
-
-* --iter <int> Maximum number of iterations in BFS search for paths between scaffolds.
-
-* --max_extensions <int> Maximum number of extensions performed between contig/scaffold ends.
-
-* -e <int> The least amount of witness links that is needed to create a link edge in graph (one for each library)
-
-* -y Extend scaffolds with smaller contigs (default on).
-
-* --no_score Do not perform statistical scoring, only run path search between contigs.
-
-* --score_cutoff <float> Only consider paths with score > score_cutoff (default 1.5)
-
-
-
-#### Under construction / proven unstable ####
-
-* -g < Haplotype detection function on or off > ( default = 0 (off) <0 or 1> )
-
-* -a < Maximum length difference ratio for merging of haplotypic regions> (float nr)
-
-* -b < Nr of standard deviations over mean/2 of coverage to allow for clasification of haplotype> (integer value)
-
-* -q < optinal flag > Parallellize work load of path finder module in case of multiple processors available using multiprocessing library for pyhton.
-
-
-NOTE2:
--------
-
-1. Definition of insert size: BESST assumes the following definitions:
- * insert size = fragment length.
- * For PE:
-```
- s t
- ------> <-------
-```
-from s to t, that is, insertsize = readlen1 + gap + readlen2. So when mean and/or threshold is supplied, it should be mean and threshold of this distance.
-
-2. Mapping reads: If you want to map a mate pair library, you will need to map them as paired end library i.e. forward-reverse mode. All read pair libraries should be in this order.
-
-3. Order of scaffolding: It is crucial for the algorithm that you give the libraries in increasing order of the insert size.
-
-
diff --git a/external/gatb-minia-pipeline/BESST/docs/VERSIONS.txt b/external/gatb-minia-pipeline/BESST/docs/VERSIONS.txt
deleted file mode 100644
index d329ff05c4da5742d74d2d43dfeebf2835355912..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/docs/VERSIONS.txt
+++ /dev/null
@@ -1,129 +0,0 @@
-VERSIONS
-----------
-
-Some versions are only included for history purposes (within () ).
-
-(V0.5
- * Added parameter prefix -o <path> that gives the user ability to choose his own output directory
- * Added required parameter -r that is integers denoting the mean read length
- * Added optional parameter -s that lets you specify the standard deviation of the library (one for each library). If specified, the gap size is calculated with a sophisticated formula. Else, it's calculated naively.
- * Added output of a gff version 3 file
- * Added so -t parameter chan take different values for diff. libraries)
-
-
-V0.6
- BUG FIXES
- * fixed bug in -e parameter, before some special cases when e < parameter_value could still be included in graph and final scaffolding step. Now, no such edge will be included.
- * fixed bug in positions of contains within scaffolds
- * Fixed +1bp index bug in GFF file output
- OTHER STUFF
- * Implemented gap estimation tool. With a narrowed down interval to gap in [-2*std_dev, mean+2*std_dev]
- * Fixed so that negative gaps are set to 0 in gap estimate.
- * Fixed so that scaffolds are written out properly in scaffolds.fa (no abutting contigs when we have negative gaps).
- * Outputs number of links between contigs to the GFF file (that gave rise to the edge in the graph).
- * -e parameter is now set independently set for each library e.g. -e 5 5 10 5 3
- * non-naive gap estimation is only active if nr of links is >= 5, independent of what -e is set to.
- * Gap fragments added to GFF file
- * Scaffolds are printed out with 60 characters per line
- * More information is printed to stdout: all parameters specified for each library
-
-V0.7
-
-* Fixed various minor bugs.
-* Changed way to create edges from BAM file, more paired-reads are now used.
-* Removed some reads that are not unique by looking at tags specified by BWA (mapping quality > 10)
-* Implemented coverage attribute for each contig.
-* Implemented repeat removal based on the coverage information for a contig.
-* Restructured code when passing function arguments between functions. Now, we have a new object caller Parameter that stores this to make the code more readable.
-* Haplotype detector
-* Removed required parameter -m (made optional). If not specified, it is calculated from the BAM file.
-* Removed required parameter -s (made optional). If not specified, it is calculated from the BAM file.
-* Removed required parameter -T (made optional). Set by program default -T = mean + 4*std_dev
-* Removed required parameter -t.
-* Added optional parameter -k. Consider contigs larger than -k at each step. Default set to: mean + (std_dev/mean)*std_dev
-* Added optional parameter -g. Detect and treat haplotypes, default value of g is 1 , i.e. function is on. To switch off, set -g 0
-* Added optional parameter -d Detect and remove duplicates, default value of g is 1 , i.e. removing duplicates. To switch off, set -g 0. Removeing dupl. based on identical mapping positions for both reads in pair (this will give some false positives)
-* Removed matplotlib dependency
-* Removed scipy,numpy dependency by using closed formula approximation for erf(x)
-* Print out scaffolds created for each pass in the algorithm
-
-V1.0
-* Various bug fixes
-* Implemented scaffolding with smaller contigs by searching for coherent paths
-* New score on edges in scaffold graph
-* a beta version of parallelization of the small contains connection finder. specified by option -q 1 (default 0).
-
-
-V1.0.1
-* Fixed bug in libmetrics.py line, MaxObsDist was only called with 1 argument here when 2 args are required. Thanks Anthony Bretaudeau.
-* Added a package for fixing split allele contigs before scaffolding in high heterozyosity diploid assemblies. (preliminary implementation)
-* Added a python script to map reads to contigs (or a genome) with BWA. It outputs a sorted .bam and a .bai file, i.e. what is needed for BESST. The script requires that bwa is installed and in the path.
-
-V1.0.2
-* Better errorwarning handling with searate module "errorhandle" for throwing exceptions/warnings.
-* Updated pysam dependency to pysam0.7
-* Changed module for parsing arguments in python. From the deprecated "optparse" to "argparse".
-* Not giving an exception if finding contigs present in BAM file but not in fasta file. Just throw a warning.
-
-V1.0.3
-* More information of scaffolding run given to "Statistics.txt".
-* Added flag -plots for plotting various histograms such as coverage of library onto contigs, score distribution of links e.t.c.
-* Fixed bug in score choosing function
-
-V1.0.3.1
-*Module plots has max number of observations 10000 due to time issues of plotting if large number of contigs or edges.
-
-V1.0.3.2
-* Made number of iterations performed in breadth first search a parameter instead of fixed to 1000.
-* Changed dispersity score of links. (explained in manual)
-*fixed bug in plotting.
-
-V1.0.4
-* Fixed bug in dispersity score (a KS test from scipy)
-* No decision of path is made if scores are similar (breaks paths)
-* Added dotplots of number of links to dispersity score for verification.
-* BESST now has dependency of scipy. Added this to setup script
-
-V1.0.4.1
-*Added gap adjustment for Francesco
-
-V1.0.4.2
-* Fixed bug in removing 0 score edges i G_prime. Now all edges in G are also removed in G_prime when searching for paths. This is an important fix.
-
-V1.1
-* Added LP solution to fix errors in orderings of small contigs when PE contamination in MP libraries are present. This is a big weakness in earlier versions (for fragmented assemblies scaffolded with MP libraries with considerable amount of PE contamination).
-
-* Gap size estimations in non linear scaffold regions are now estimated with a LP module toghether with GapEst. Since the theory of gapest (analytic derivation, hence the speed) only works for one gap between two scaffolds, all gaps were previously estimated one by one with GapEst. Now, in nonlinear regions, gaps between all pairs of scaffolds are estimated. These estimations are then given as input in the objective function for an linear programming instance. The onbejtive is to minimize the total distance of a current solution to the LP, given GapEst estimated ones. This will give more robust esitmations in case where short contigs and few links by making use of more information simultaneosly.
-
-* Added a histogram of estimated gap distribution in cas -plots are specified.
-
-* If a gap estiamtion is less than or equal to 0, a single lower case 'n' is output between contigs (changed from a single 'N'). This is changed to try to standardize the output of scaffolders (SSPACE output 'n'). Also after discussion with QUAST (assembly evaluating software) author Alexey to be able to parse scaffold output consistently.
-
-* pulp (Linear programming module for python) is added as required packages
-
-* added parameter --separate_repeats to separate potential repeats (inferred by BESST) into a file "repeats.fa". This was default output for BESST in earlier versions. Now, default output is a single file in each scaffolding step Scaffolds_passX.fa.
-
-* added parameter -filter_contigs <int> . This parameter with remove att contigs smaller than <int> from all scaffolding (and scaffold output).
-
-* added parameter --no_score. If specified, statistical scoring is not used to scaffold. BESST instead relies soley on the new LP module to search for paths between contigs. The effect of this is not thouroughly tested so far but preliminary results hint that it is slower but gives slightly better results.
-
-V1.2
-* BESST can now parse alignments of both forward reverse and reverse forward orientation. To specify the orientation of the alignments, a parameter --orientation is added. --orientation takes a string 'rf' or 'fr' for each library that is povided with the -f option to BESST. If --orientation is not specified, BESST throws a warning that orientations are not specified and proceeds by assuming that the alignemts are done with fr orientation irregardless of library (as is done in previous versions). This is done not to break old pipelines.
-
-* Added automatic check for which scaffolding approach that are the most sound/beneficial given the library and the fragmentation level of the assembly (statistical scoring or pathsearching immediately).
-
-* relaxed dependency criterion on pysam. Now, all versions >=0.7 works (bug when installing with pysam v0.7 reported by Shaun Jackman).
-
-* Some minor bugs and fixes implemented by Rayan Chikhi, Jan van Haarst and Mattias Frånberg.
-
-V1.3
-
-* MAJOR IMPROVEMENTS IN RUNTIME AND MEMORY CONSUMPTION. It is strongly encouraged to update to this version (or later) for bigger assemblies.
-
-* Removed dependency on PuLP. LP is now solved with module from https://github.com/pv/scipy-work/blob/11c7f50e8b90edb1e74e5f0c6710717b2af6aed6/scipy/optimize/_lp.py
-
-* Added paramenters --max_extensions, --score_cutoff. Good to set if millons of contigs in assembly (see docs/manual.md).
-
-* Added merging of overlapping k-mers in contigs for final output
-
-
diff --git a/external/gatb-minia-pipeline/BESST/docs/figures/isize_narrow_cont.png b/external/gatb-minia-pipeline/BESST/docs/figures/isize_narrow_cont.png
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diff --git a/external/gatb-minia-pipeline/BESST/docs/figures/isize_wide_cont.pdf b/external/gatb-minia-pipeline/BESST/docs/figures/isize_wide_cont.pdf
deleted file mode 100644
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diff --git a/external/gatb-minia-pipeline/BESST/docs/figures/isize_wide_cont.png b/external/gatb-minia-pipeline/BESST/docs/figures/isize_wide_cont.png
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diff --git a/external/gatb-minia-pipeline/BESST/runBESST b/external/gatb-minia-pipeline/BESST/runBESST
deleted file mode 100755
index f3128c7bc26bfccad8cbea9492ff9b1e959d944a..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/runBESST
+++ /dev/null
@@ -1,410 +0,0 @@
-#!/usr/bin/env python
-'''
- BESST - Scaffolder for genomic assemblies
- Copyright (C) 2013 Kristoffer Sahlin
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-'''
-
-import sys
-import os
-import errno
-from time import time
-import argparse
-import shutil
-from itertools import izip
-
-from BESST import errorhandle
-from BESST import decide_approach
-
-def mkdir_p(path):
- try:
- os.makedirs(path)
- except OSError as exc: # Python >2.5
- if exc.errno == errno.EEXIST and os.path.isdir(path):
- pass
- else: raise
-
-def ReadInContigseqs(contigfile,contig_filter_length, Information):
- cont_dict = {}
- k = 0
- temp = ''
- accession = ''
- for line in contigfile:
- if line[0] == '>' and k == 0:
- accession = line[1:].strip().split()[0]
- cont_dict[accession] = ''
- k += 1
- elif line[0] == '>':
- cont_dict[accession] = temp
- temp = ''
- accession = line[1:].strip().split()[0]
- else:
- temp += line.strip()
- cont_dict[accession] = temp
-
- # for contig in cont_dict.keys():
- # print 'Initial length:', len(cont_dict[contig])
- if contig_filter_length:
- singled_out = 0
- for contig in cont_dict.keys():
- if len(cont_dict[contig]) < contig_filter_length:
- del cont_dict[contig]
- singled_out += 1
- print >> Information, 'Number of contigs discarded from further analysis (with -filter_contigs set to {0}): {1}'.format(contig_filter_length,singled_out)
- return(cont_dict)
-
-def main(options):
- import pysam
-
- from BESST import Parameter
- from BESST import CreateGraph as CG
- from BESST import MakeScaffolds as MS
- from BESST import GenerateOutput as GO
- from BESST import libmetrics
- #from BESST import bam_parser
- from BESST.diploid import get_haplotype_regions
-
- tot_start = time()
- Contigs = {} # contig dict that stores contig objects
- Scaffolds = {} # scaffold dict with contig objects for easy fetching of all contigs in a scaffold
- small_contigs = {}
- small_scaffolds = {}
-
- param = Parameter.parameter() # object containing all parameters (user specified, defaulted and comuted along the way.)
- param.scaffold_indexer = 1 # global indicator for scaffolds, used to index scaffolds when they are created
- param.multiprocess = options.multiprocess
- param.no_score = options.no_score
- param.score_cutoff = options.score_cutoff
- param.max_extensions = options.max_extensions
- param.NO_ILP = options.NO_ILP
- param.FASTER_ILP = options.FASTER_ILP
- param.bfs_traversal = options.bfs_traversal
- param.print_scores = options.print_scores
- param.min_mapq = options.min_mapq
-
- if args.devel:
- h = guppy.hpy()
- initial = h.heap()
- print 'Initial:\n{0}'.format(initial)
-
-
- param.development = options.devel
- options.output = options.output + '/BESST_output'
-
- mkdir_p(options.output)
- if options.plots:
- mkdir_p(os.path.join(options.output, 'plots'))
-
- param.information_file = open(options.output + '/Statistics.txt', 'w')
- param.plots = options.plots
- Information = param.information_file
- open(options.output + '/haplotypes.fa', 'w')
- #Read in the sequences of the contigs in memory
- start = time()
- C_dict = ReadInContigseqs(open(options.contigfile, 'r'), options.contig_filter_length, Information)
-
- elapsed = time() - start
- print >> Information, 'Time elapsed for reading in contig sequences:' + str(elapsed) + '\n'
-
- print 'Number of initial contigs:', len(C_dict)
- if options.devel:
- h = guppy.hpy()
- after_ctgs = h.heap()
- print 'After ctg seqs:\n{0}'.format(after_ctgs)
-
- if options.haplotype:
- get_haplotype_regions.main(options.output, C_dict, options.kmer, options.mmer, 0.8)
- sys.exit()
- #iterate over libraries
- param.first_lib = True
- param.path_threshold = options.path_threshold
- for i in xrange(len(options.bamfiles)):
- param.pass_number = i+1
- param.bamfile = options.bamfiles[i]
- param.orientation = options.orientation[i] if options.orientation != None else 'fr'
- param.mean_ins_size = options.mean[i] if options.mean != None else None
- param.ins_size_threshold = options.threshold[i] if options.threshold != None else None
- param.edgesupport = options.edgesupport[i] if options.edgesupport != None else 3
- param.read_len = options.readlen[i] if options.readlen != None else None
- param.output_directory = options.output
- param.std_dev_ins_size = options.stddev[i] if options.stddev != None else None
- param.contig_threshold = options.minsize[i] if options.minsize != None else None
- param.cov_cutoff = options.covcutoff[i] if options.covcutoff != None else None
- param.hapl_ratio = options.haplratio
- param.hapl_threshold = options.haplthreshold
- param.detect_haplotype = options.haplotype
- param.detect_duplicate = options.duplicate
- param.extend_paths = options.extendpaths
- print >> Information, '\nPASS ' + str(i + 1) + '\n\n'
-
- #get library statistics
- with pysam.Samfile(param.bamfile, 'rb') as bam_file:
- #if param.first_lib:
- #print bam_file.references
- #print map(bam_file.gettid, bam_file.references)
- start = time()
- param.contig_index = dict(izip(xrange(len(bam_file.references)), bam_file.references))
- libmetrics.get_metrics(bam_file, param, Information)
-
- elapsed = time() - start
- print >> Information, 'Time elapsed for getting libmetrics, iteration ' + str(i) + ': ' + str(elapsed) + '\n'
-
-
- if args.devel:
- h = guppy.hpy()
- after_libmetrics = h.heap()
- print 'After libmetrics\n{0}\n'.format(after_libmetrics)
-
- #create graph
- print 'Creating contig graph with library: ', param.bamfile
- start = time()
- (G, G_prime) = CG.PE(Contigs, Scaffolds, Information, C_dict, param, small_contigs, small_scaffolds, bam_file) #Create graph, single out too short contigs/scaffolds and store them in F
- elapsed = time() - start
- print >> Information, 'Total time for CreateGraph-module, iteration ' + str(i) + ': ' + str(elapsed) + '\n'
- decide_approach.decide_scaffolding_procedure(Scaffolds,small_scaffolds, param)
-
- if args.devel:
- h = guppy.hpy()
- after_ctg_graph = h.heap()
- print 'After contig graph\n{0}\n'.format(after_ctg_graph)
-
- #print G, not G == None, not None, None == False
- if not G and not param.no_score:
- print '0 contigs/super-contigs passed the length criteria of this step. Exiting and printing results.. '
-
-
- print 'Constructed contig graph. Start BESST algorithm for creating scaffolds. '
- start = time()
- MS.Algorithm(G, G_prime, Contigs, small_contigs, Scaffolds, small_scaffolds, Information, param) # Make scaffolds, store the complex areas (consisting of contig/scaffold) in F, store the created scaffolds in Scaffolds, update Contigs
- elapsed = time() - start
- print >> Information, 'Time elapsed for making scaffolds, iteration ' + str(i) + ': ' + str(elapsed) + '\n'
-
- print 'Writing out scaffolding results for step', i + 1, ' ...'
-
- F = [] #list of (ordered) lists of tuples containing (contig_name, direction, position, length, sequence). The tuple is a contig within a scaffold and the list of tuples is the scaffold.
- for scaffold_ in small_scaffolds:
- S_obj = small_scaffolds[scaffold_]
- list_of_contigs = S_obj.contigs #list of contig objects contained in scaffold object
- F = GO.WriteToF(F, small_contigs, list_of_contigs)
- for scaffold_ in Scaffolds.keys(): #iterate over keys in hash, so that we can remove keys while iterating over it
- ### Go to function and print to F
- ### Remove Scaf_obj from Scaffolds and Contig_obj from contigs
- S_obj = Scaffolds[scaffold_]
- list_of_contigs = S_obj.contigs # List of contig objects contained in scaffold object
- F = GO.WriteToF(F, Contigs, list_of_contigs)
-
-
- GO.PrintOutput(F, Information, param.output_directory, param, i + 1)
-
- if not options.separate_repeats:
- destination = open("{0}/pass{1}/Scaffolds_pass{1}.fa".format(param.output_directory, str(i+1) ), 'wb')
- #destination = open(outfile,'wb')
- shutil.copyfileobj(open("{0}/pass{1}/Scaffolds-pass{1}.fa".format(param.output_directory, str(i+1) ), 'rb'), destination)
- shutil.copyfileobj(open("{0}/repeats.fa".format(param.output_directory, str(i+1) ), 'rb'), destination)
- destination.close()
- os.remove( "{0}/pass{1}/Scaffolds-pass{1}.fa".format(param.output_directory, str(i+1)) )
-
- param.first_lib = False #not the first lib any more
-
- if not options.separate_repeats:
- os.remove( "{0}/repeats.fa".format(param.output_directory ) )
-
- ### Calculate stats for last scaffolding step
- scaf_lengths = [Scaffolds[scaffold_].s_length for scaffold_ in Scaffolds.keys()]
- sorted_lengths = sorted(scaf_lengths, reverse=True)
- scaf_lengths_small = [small_scaffolds[scaffold_].s_length for scaffold_ in small_scaffolds.keys()]
- sorted_lengths_small = sorted(scaf_lengths_small, reverse=True)
- N50, L50 = CG.CalculateStats(sorted_lengths, sorted_lengths_small, param, Information)
- param.current_L50 = L50
- param.current_N50 = N50
-
- elapsed = time() - tot_start
- print >> Information, 'Total time for scaffolding: ' + str(elapsed) + '\n'
-
- print 'Finished\n\n '
-
- return()
-
-
-
-parser = argparse.ArgumentParser(prog='BESST', description="BESST - scaffolder for genomic assemblies.", epilog='''Source code and manual: http://github.com/ksahlin/BESST\n\nPlease cite:\nSahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) BESST--efficient scaffolding of large fragmented assemblies. BMC Bioinformatics 15, 281\n''', formatter_class=argparse.RawDescriptionHelpFormatter)
-
-required = parser.add_argument_group('Required arguments')
-libstats = parser.add_argument_group('Library information', 'Library parameters that can be set, e.g., read length, insert size mean/std_dev, coverage etc.')
-haplotypes = parser.add_argument_group('Ploidy', 'Options involving detection of split allele contigs in diploid assemblies.')
-parameters = parser.add_argument_group('Parameters/variables/threshold involved in BESST.')
-other = parser.add_argument_group('Various other parameters')
-group = parser.add_mutually_exclusive_group(required=False)
-
-## required
-required.add_argument("-c", dest="contigfile", type=str, required=True,
- help="Fasta file containing contigs.")
-
-required.add_argument("-f", dest="bamfiles", type=str, nargs='+', required=True,
- help="Path(s) to bamfile(s).")
-
-
-## libstats
-
-libstats.add_argument("-r", dest="readlen", type=int, nargs='+',
- help="Mean read length of libraries. ")
-
-libstats.add_argument("-m", dest="mean", type=float, nargs='+',
- help="Mean insert size of libraries.")
-
-libstats.add_argument("-s", dest="stddev", type=float, nargs='+',
- help="Estimated standard deviation of libraries.")
-
-libstats.add_argument("-z", dest="covcutoff", type=int, nargs='+',
- help="User specified coverage cutoff. (Manually filter \
- out contigs with coverage over this value)")
-
-
-## parameters
-
-parameters.add_argument("-T", dest="threshold", type=int, nargs='+',
- help="Threshold value filter out reads that are mapped too far apart given insert size. ")
-
-parameters.add_argument("-e", dest="edgesupport", type=int, nargs='+',
- help="Threshold value for the least nr of links that is needed to create an edge. Default for all libs: 5 ")
-
-parameters.add_argument("-k", dest="minsize", type=int, nargs='+',
- help="Contig size threshold for the library (all contigs below this size is discarded from the \
- 'large contigs' scaffolding, but included in pathfinding). Default: Set to same as -T parameter")
-
-parameters.add_argument("-filter_contigs", dest="contig_filter_length", type=int, default=None,
- help="Contigs under this size is discarded from all scaffolding (including pathfinding).\
- they are also not included in the resulting scaffold output fasta file and any\
- of the other files as well as all statistics. Default: All contigs are included")
-
-parameters.add_argument("--min_mapq", dest="min_mapq", type=int, default=11,
- help="Lowest mapping quality allowed in order to use the read pair (both reads needs to have equal or bigger mapq than this value). This value is compared to the mapping quality column in the BAM file. ")
-
-
-parameters.add_argument("--iter", dest="path_threshold", type=int, default=100000,
- help="The number of iterations performed in breadth first search for placing smaller contigs. ")
-
-parameters.add_argument("--score_cutoff", dest="score_cutoff", type=float, default=1.5,
- help="Only store paths with score larger than score_cutoff. ")
-
-parameters.add_argument("--max_extensions", dest="max_extensions", type=int,
- help="Maximum number of (large) scaffolds to search for paths extensions with. ")
-
-other.add_argument("--bfs_traversal", dest="bfs_traversal", action="store_true",
- help="Choose a breadth first search in the contig graph. Default is using the extenstion with the most \
- links to investigate first (Sort of depth first-ish)",)
-
-
-## related to scaffolding high heterozygozity assemblies with lots of split haplotype contigs
-
-haplotypes.add_argument("-a", dest="haplratio", type=float, default=1.3,
- help="Maximum length ratio for merging of haplotypic regions.")
-
-haplotypes.add_argument("-b", dest="haplthreshold", type=int, default=3,
- help="Number of standard deviations over mean/2 of coverage to allow for clasification of haplotype.\
- Example: contigs with under mean/2 + 3sigma are indicated as potential haplotypes (tested later) \
- if -b 3")
-
-other.add_argument("-K", dest="kmer", type=int, default=50,
- help="k-mer size used in de brujin graph for obtaining contigs in assembly, default 50")
-
-other.add_argument("-M", dest="mmer", type=int, default=40,
- help="m-mer usted for creating connection graph. Should be set lower than k-mer size ")
-
-haplotypes.add_argument("-g", dest="haplotype", action="store_true",
- help="Haplotype detection function, default = off")
-
-
-## other
-
-required.add_argument("--orientation", dest="orientation", type=str, nargs='+',
- help="Mapped orientation for each library given with -f option. Valid input is either fr (forward reverse orientation) or rf (reverse forward orientation).")
-
-other.add_argument("-o", dest="output", type=str, default='.',
- help="Path to output directory. BESST will create a folder named 'BESST_output' in the directory given by the path.")
-
-other.add_argument("-d", dest='duplicate' , action="store_false",
- help="Deactivate sequencing duplicates detection")
-
-group.add_argument("-y", dest='extendpaths', action="store_false",
- help="Deactivate pathfinder module for including smaller contigs.")
-
-other.add_argument("-q", dest="multiprocess", action="store_true",
- help="Parallellize work load of path finder module in case of multiple processors available.\
- ",)
-
-group.add_argument("--no_score", dest="no_score", action="store_true",
- help="Statistical scoring is not performed. BESST instead searches for paths between contigs.\
- ",)
-
-other.add_argument("-devel", action="store_true",
- help="Run in development mode (bug checking and memory usage etc.)")
-
-other.add_argument("-plots", action="store_true",
- help="Plot coverage, histograms of scores e.t.c.")
-
-other.add_argument("--separate_repeats", dest="separate_repeats", action="store_true",
- help="Separates contigs classified as repeats by BESST into a file 'repeats.fa'. They are \
- not included in the main scaffolding output file with this flag specified.")
-
-parameters.add_argument("--NO_ILP", dest="NO_ILP", action="store_true",
- help="Warning: Do not use this option! This option is included only for benchmarking purposes of old BESST algorithm. This option will give poor results as it mimics earlier versions of BESST.")
-
-parameters.add_argument("--FASTER_ILP", dest="FASTER_ILP", action="store_true",
- help="Faster but worse performing heuristic solution to solving ILPs. May be used if BESST is too slow. However, lowering --iter is usually more effective to reduce scaffolding time.")
-
-parameters.add_argument("--print_scores", dest="print_scores", action="store_true",
- help="Print BESST scores on edges in the Scaffolding graph.")
-
-
-other.add_argument('--version', action='version', version='%(prog)s 2.0.0')
-
-
-
-
-if len(sys.argv) == 1:
- sys.argv.append('-h')
-
-args = parser.parse_args()
-
-errorhandle.check_module('mathstats')
-errorhandle.parse_check(args, parser)
-
-if args.devel:
- import guppy
-
-if args.plots:
- try:
- import matplotlib
- matplotlib.use('Agg')
- import matplotlib.pyplot as plt
- except ImportError:
- args.plots = False
-
-
-##
-# Call BESST algorithm
-
-main(args)
-
-if args.devel:
- h = guppy.hpy()
- at_end= h.heap()
-
- print 'At end:\n{0}\n'.format(at_end)
-
-
-
diff --git a/external/gatb-minia-pipeline/BESST/scripts/besst/test_lp.py b/external/gatb-minia-pipeline/BESST/scripts/besst/test_lp.py
deleted file mode 100644
index 27c1943b7efc92e6d5e50d9c3f6df3daee623541..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/scripts/besst/test_lp.py
+++ /dev/null
@@ -1,119 +0,0 @@
-######### Unit test section #########
-from numpy import *
-from numpy.testing import *
-
-from BESST.lp_solve import lp_solve
-
-def test_lp(prt=False):
- m1 = 20
- m2 = 50
- probs = [
- {
- 'A': array([
- [2., 5., 3., -1., 0., 0.],
- [3., 2.5, 8., 0., -1., 0.],
- [8.,10., 4., 0., 0., -1.]]),
- 'b': array([185., 155., 600.]),
- 'c': array([4., 8., 3., 0., 0., 0.]),
- 'result': [
- array([ 66.25, 0., 17.5, 0., 183.75, 0.]),
- 317.5,
- True,
- True,
- array([2, 0, 4])
- ]
- },
- {
- 'A': array([
- [-1., -1., -1., 0., 0., 0.],
- [ 0., 0., 0., 1., 1., 1.],
- [ 1., 0., 0., 1., 0., 0.],
- [ 0., 1., 0., 0., 1., 0.],
- [ 0., 0., 1., 0., 0., 1.]]),
- 'b': array([-0.5, 0.4, 0.3, 0.3, 0.3]),
- 'c': array([2.8, 6.3, 10.8, -2.8, -6.3, -10.8]),
- 'result': [
- array([0.3, 0.2, 0.0, 0.0, 0.1, 0.3]),
- -1.77,
- True,
- True,
- array([1, 7, 0, 4, 5])
- ]
- },
- { # with degeneracy
- 'A': array([[cos(2*pi*i/(m1+1))-1., sin(2*pi*i/(m1+1))]
- for i in xrange(1,m1+1)]).T,
- 'b': zeros(2).T,
- 'c': -ones(m1).T,
- 'result': [
- zeros(m1),
- 0.,
- True,
- True,
- array([0,19])
- ]
-
- },
- { # with unboundedness (0 is a member of the convex hull
- # of these vectors)
- 'A': array([[cos(2*pi*i/(m2+1))-1., sin(2*pi*i/(m2+1))]
- for i in xrange(0,m2)]).T,
- 'b': zeros(2).T,
- 'c': -ones(m2).T,
- 'result': [
- None, # unchecked when unbounded
- -Inf, # unchecked when unbounded
- False,
- True,
- array([2, 49])
- ]
-
- },
- { # Unsolvable
- 'A': array([[cos(2*pi*i/(m2+1))-1., sin(2*pi*i/(m2+1))]
- for i in xrange(0,m2)]).T,
- 'b': ones(2).T,
- 'c': -ones(m2).T,
- 'result': [
- None, # unchecked when unsolvable
- None, # unchecked when unsolvable
- None, # unchecked when unsolvable
- False,
- array([50, 1])
- ]
-
- }, # add other test cases here...
- ]
-
-
- for prob in probs:
- lpsol = lp_solve(prob['c'],prob['A'],prob['b'])
- optx = lpsol.x
- zmin = lpsol.fun
- bounded = lpsol.is_bounded
- solvable = lpsol.is_solvable
- basis = lpsol.basis
- if prt:
- print "A:\n",prob['A']
- print "b:",prob['b']
- print "c:",prob['c']
- print " ---->"
- print "optx:",optx
- print "zmin:",zmin
- print "bounded:",bounded
- print "solvable:",solvable
- print "basis:",basis
- print "-------------------------------------------"
- else:
- expected_res = prob['result']
- assert_equal(solvable, expected_res[3], err_msg=repr(prob))
- assert_equal(basis, expected_res[4], err_msg=repr(prob))
- if solvable:
- assert_equal(bounded, expected_res[2], err_msg=repr(prob))
- if bounded:
- assert_almost_equal(optx, expected_res[0],
- err_msg=repr(prob))
- assert_almost_equal(zmin, expected_res[1], err_msg=repr(prob))
- # when unbounded zmin == -Inf, but -Inf != -Inf
- # so we won't check it...
-test_lp(True)
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py b/external/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py
deleted file mode 100644
index a37f3281f9297cf6b670fe9344aa26da7f7f306e..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py
+++ /dev/null
@@ -1,324 +0,0 @@
-#!/usr/bin/env python
-'''
-Created on Jul 25, 2013
-Modified on Oct 30, 2015
-
-@author: ksahlin
-@author: sidorov-si
-'''
-import argparse
-import os
-import shutil
-import subprocess
-import sys
-import tempfile
-from datetime import datetime
-from sys import stdout
-import pysam
-
-
-##
-# Converts a sam file to a bam file using pysam.
-#
-# @param sam_path Path of the .sam file.
-# @param bam_path Path of the resulting .bam file.
-#
-def sam_to_bam(sam_path, bam_path):
- sam_file = pysam.Samfile(sam_path, "r")
- bam_file = pysam.Samfile(bam_path, "wb", template=sam_file)
-
- for alignment in sam_file:
- bam_file.write(alignment)
-
-
-##
-# Maps the given paired end reads using bwa, and writes a
-# sorted .bam file in the given output file.
-#
-# @param pe1_path Path of the first reads.
-# @param pe2_path Path of the second reads.
-# @param genome_path Path to the reference genome.
-# @param output_path Path of the output file without extension ".bam".
-#
-def bwa_sampe(pe1_path, pe2_path, genome_path, output_path, tmp_dir, bwa_path, clear_tmp):
- print
- print 'Aligning with bwa aln/sampe.'
- stdout.flush()
- start = datetime.now()
- work_dir = tempfile.mkdtemp() if tmp_dir == None else tmp_dir
- genome_db = os.path.join(work_dir, "genome")
- pe1_output = os.path.join(work_dir, "pe1.sai")
- pe2_output = os.path.join(work_dir, "pe2.sai")
- bwa_output = os.path.join(work_dir, "output.sam")
- stderr_file = open(output_path + '.bwa.1', 'w')
- print 'Temp directory:', work_dir
- print 'Output path: ', output_path
- print 'Stderr file: ', output_path + '.bwa.1'
- stdout.flush()
-
- print 'Make bwa index...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "index", "-p", genome_db, genome_path ], stderr=stderr_file)
- print 'Done.'
- stdout.flush()
- with open(pe1_output, "w") as pe1_file:
- print 'Align forward reads with bwa aln...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "aln", "-t 8", genome_db, pe1_path ],
- stdout=pe1_file, stderr=stderr_file)
- print 'Done.'
- stdout.flush()
-
- with open(pe2_output, "w") as pe2_file:
- print 'Align reverse reads with bwa aln...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "aln", "-t 8", genome_db, pe2_path ],
- stdout=pe2_file, stderr=stderr_file)
- print 'Done.'
- stdout.flush()
-
- with open(bwa_output, "w") as bwa_file:
- print 'Start bwa sampe...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "sampe",
- genome_db,
- pe1_output, pe2_output,
- pe1_path, pe2_path ], stdout=bwa_file, stderr=stderr_file)
- print 'Done.'
- stdout.flush()
-
- elapsed = datetime.now() - start
- print 'Time elapsed for bwa index and aln/sampe:', elapsed
-
- print
- print 'Convert SAM to BAM...',
- stdout.flush()
- start = datetime.now()
- sam_to_bam(bwa_output, bwa_output + ".bam")
- if clear_tmp:
- os.remove(bwa_output)
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for SAM to BAM conversion:', elapsed
-
- print
- print 'Sort BAM...',
- stdout.flush()
- start = datetime.now()
- pysam.sort(bwa_output + ".bam", output_path)
- if clear_tmp:
- os.remove(bwa_output + ".bam")
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for BAM sorting:', elapsed
-
- print
- print 'Index BAM...',
- stdout.flush()
- start = datetime.now()
- pysam.index(output_path + '.bam')
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for BAM indexing:', elapsed
-
- print
- print 'Remove temp files...',
- stdout.flush()
- start = datetime.now()
- shutil.rmtree(work_dir)
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for temp files removing:', elapsed
- stdout.flush()
-
-
-def bwa_mem(pe1_path, pe2_path, genome_path, threads, output_path, tmp_dir, bwa_path, clear_tmp):
- print
- print 'Aligning with bwa mem.'
- stdout.flush()
- start = datetime.now()
- work_dir = tempfile.mkdtemp() if tmp_dir == None else tmp_dir
- genome_db = os.path.join(work_dir, "genome")
- pe1_output = os.path.join(work_dir, "pe1.sai")
- pe2_output = os.path.join(work_dir, "pe2.sai")
- bwa_output = os.path.join(work_dir, "output.sam")
- stderr_file = open(output_path + '.bwa.1', 'w')
- print 'Temp directory:', work_dir
- print 'Output path: ', output_path
- print 'Stderr file: ', output_path + '.bwa.1'
- stdout.flush()
-
- print 'Make bwa index...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "index", "-p", genome_db, genome_path ], stderr=stderr_file)
- print 'Done.'
- stdout.flush()
- with open(bwa_output, "w") as bwa_file:
- print 'Align with bwa mem...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "mem", "-t", threads,
- genome_db, pe1_path, pe2_path ],
- stdout=bwa_file,
- stderr=stderr_file)
- print 'Done.'
- stdout.flush()
-
- elapsed = datetime.now() - start
- print 'Time elapsed for bwa index and mem: ', elapsed
-
- print
- print 'Convert SAM to BAM...',
- stdout.flush()
- start = datetime.now()
- sam_to_bam(bwa_output, bwa_output + ".bam")
- if clear_tmp:
- os.remove(bwa_output)
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for SAM to BAM conversion:', elapsed
-
- print
- print 'Sort BAM...',
- stdout.flush()
- start = datetime.now()
- pysam.sort(bwa_output + ".bam", output_path)
- if clear_tmp:
- os.remove(bwa_output + ".bam")
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for BAM sorting:', elapsed
-
- print
- print 'Index BAM...',
- stdout.flush()
- start = datetime.now()
- pysam.index(output_path + '.bam')
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for BAM indexing:', elapsed
-
- print
- print 'Remove temp files...',
- stdout.flush()
- start = datetime.now()
- shutil.rmtree(work_dir)
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for temp files removing:', elapsed
- stdout.flush()
-
-
-def map_single_reads(pe_path, genome_path, output_path, bwa_path):
- print
- print 'Aligning with bwa aln/samse.'
- stdout.flush()
- start = datetime.now()
- work_dir = tempfile.mkdtemp()
- genome_db = os.path.join(work_dir, "genome")
- pe_output = os.path.join(work_dir, "pe.sai")
- bwa_output = os.path.join(work_dir, "output.sam")
- print 'Temp directory:', work_dir
- print 'Output path: ', output_path
- print 'Stderr file: /dev/null'
- stdout.flush()
-
- null = open("/dev/null")
- print 'Make bwa index...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "index", "-p", genome_db, genome_path ], stderr=null)
- print 'Done.'
- stdout.flush()
- with open(pe_output, "w") as pe_file:
- print 'Align with bwa aln...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "aln", genome_db, pe_path ], stdout=pe_file, stderr=null)
- print 'Done.'
- stdout.flush()
-
- with open(bwa_output, "w") as bwa_file:
- print 'Start bwa samse...',
- stdout.flush()
- subprocess.check_call([ bwa_path, "samse",
- "-r", "@RG\tID:ILLUMINA\tSM:48_2\tPL:ILLUMINA\tLB:LIB1",
- genome_db,
- pe_output,
- pe_path ], stdout=bwa_file, stderr=null)
- print 'Done.'
- stdout.flush()
-
- elapsed = datetime.now() - start
- print 'Time elapsed for bwa index and aln/samse:', elapsed
-
- print
- print 'Copy the result to the output directory and remove temp files...',
- stdout.flush()
- start = datetime.now()
- shutil.move(bwa_output, output_path)
- shutil.rmtree(work_dir)
- elapsed = datetime.now() - start
- print 'Done.'
- print 'Time elapsed for copying result to the output directory and removing temp files:', elapsed
- stdout.flush()
-
-
-if __name__ == '__main__':
- parser = argparse.ArgumentParser(description="Maps the given reads with bwa.")
- parser.add_argument('pe1_path', type=str, help='Path to the first reads in a read pair (if paired reads). Just the reads if single reads')
- parser.add_argument('pe2_path', type=str, nargs='?', default=False, help='Path to the second pairs. Leave unspecified if single reads.')
- parser.add_argument('genome_path', type=str, help='Path to the reference genome/contigs.')
- parser.add_argument('output_path', type=str, help='Output path of resulting .bam and .bai file.')
- parser.add_argument('--tmp_path', type=str, required=False, help='Output path of temporary files.')
- parser.add_argument('--bwa_path', type=str, default='bwa', required=False, help='Path to bwa binary with bwa binary name at the end.')
- parser.add_argument('--threads', type=str, default='8', required=False, help='Number of threads for bwa mem.')
- parser.add_argument('--clear', action="store_true", required=False,
- help='Remove SAM file when BAM is already created, and remove BAM file when sorted BAM is already created.')
- parser.add_argument('--nomem', action="store_true", required=False,
- help='bwa mem default, If flag specified the script uses old bwa algorithm with "aln" and "sampe". ')
-
- args = parser.parse_args()
-
- tmp_path = args.tmp_path
- if tmp_path != None and not os.path.exists(tmp_path):
- os.makedirs(tmp_path)
-
- output_path = args.output_path
- if not os.path.exists(output_path):
- os.makedirs(output_path)
-
- print
- print 'pe1_path:', args.pe1_path
- print 'pe2_path:', args.pe2_path
- print 'genome_path:', args.genome_path
- print 'output_path:', output_path
- if tmp_path != None:
- print "tmp_path:", tmp_path
- print 'bwa path:', args.bwa_path
- print 'number of threads:', args.threads
- print 'Remove temp SAM and BAM files:',
- if args.clear:
- print 'Yes'
- else:
- print 'No'
- print 'Use bwa aln and sampe instead of bwa mem:',
- if args.nomem:
- print 'Yes'
- else:
- print 'No'
- stdout.flush()
-
- print
- print 'Start processing.'
- stdout.flush()
- if args.pe2_path and args.nomem:
- bwa_sampe(args.pe1_path, args.pe2_path, args.genome_path, output_path, tmp_path,
- args.bwa_path, args.clear)
- elif args.pe2_path:
- bwa_mem(args.pe1_path, args.pe2_path, args.genome_path, args.threads, output_path,
- tmp_path, args.bwa_path, args.clear)
- else:
- map_single_reads(args.pe1_path, args.genome_path, args.output_path, args.bwa_path)
- print
- print 'Processing is finished.'
- stdout.flush()
-
-
diff --git a/external/gatb-minia-pipeline/BESST/setup.py b/external/gatb-minia-pipeline/BESST/setup.py
deleted file mode 100644
index 993bc45196dca107b795ea2fdabf29e386345490..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/BESST/setup.py
+++ /dev/null
@@ -1,29 +0,0 @@
-
-import os
-from setuptools import setup, find_packages
-
-setup(
- name='BESST',
- version='2.1.0',
- packages=find_packages(exclude=['ez_setup', 'examples', 'tests']),
- classifiers=[
- "Development Status :: 4 - Beta",
- "Environment :: Console",
- "Intended Audience :: Science/Research",
- "Natural Language :: English",
- "Operating System :: POSIX :: Linux",
- "Programming Language :: Python",
- "Topic :: Scientific/Engineering :: Bio-Informatics"
- ],
- scripts=['runBESST', 'scripts/reads_to_ctg_map.py'],
- description='Scaffolder for genomic assemblies.',
- author='Kristoffer Sahlin',
- author_email='kristoffer.sahlin@scilifelab.se',
- url='https://github.com/ksahlin/BESST',
- license='GPLv3',
- long_description=open(os.path.join(os.getcwdu(), 'README.md')).read(),
- install_requires=['pysam>=0.7',
- 'networkx>=1.9',
- 'mathstats>=0.2.1',
- 'scipy>=0.9'],
-)
diff --git a/external/gatb-minia-pipeline/Makefile b/external/gatb-minia-pipeline/Makefile
deleted file mode 100644
index f63eadf4966025f5ffc732cf3fce4e90991b6fef..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
-python=python # this is to enable changing python version; 'make python=/path/to/python'
-
-all:
- @#make -C superscaffolder # using a better scaffolder now
- @#make -C minia # will be dynamically compiled
- @echo "Checking Python"
- @$(python) -c "import scipy; print('scipy OK')"
- @$(python) -c "import numpy; print('numpy OK')"
- @$(python) -c "import mathstats; print('mathstats OK')"
- @$(python) -c "import pysam; print('pysam OK')"
- @echo "There is nothing to make. All programs are provided as binaries."
-
-.FORCE:
-
-test: all .FORCE
- # BESST is unable to process that small file anyway (too few alignments), so I'm skipping it
- cd test ; rm -Rf assembly* ; ../gatb -s small_test_reads.fa.gz --nb-cores 4 --kmer-sizes 21 #--no-error-correction
diff --git a/external/gatb-minia-pipeline/README.md b/external/gatb-minia-pipeline/README.md
deleted file mode 100644
index 9e8da6e5e306adb744086a6ce7741cf4d6af3c86..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/README.md
+++ /dev/null
@@ -1,80 +0,0 @@
-GATB-Minia-Pipeline
--------------
-
-GATB-Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes.
-
-It is multi-k, to aim for high contiguity. Similar software: MEGAHIT, metaSPAdes.
-
-The pipeline consists of:
-- Bloocoo (error correction)
-- Minia 3 (contigs assembly) based on the BCALM2 (unitigs assembly) tool
-- BESST (scaffolding)
-
-Prerequisites
--------------
-
-- Linux 64 bits (for Minia binary)
-
-- bwa (for BESST)
-
-- Python >= 2.7 and < 3 for BESST:
-
- * BESST
-
-BESST does not have a solid Python 3 support, hence only Pytohn 2 is supported.
-
-See next section for a quick way to install them.
-Note: these Python modules are only needed for BESST.
-You can skip them if you do not plan on performing scaffolding.
-
-Installation
-------------
-
- python2 -m pip install --user BESST
-
- git clone --recursive https://github.com/GATB/gatb-minia-pipeline
-
- cd gatb-minia-pipeline ; make test
-
-Usage
------
-
-Command line arguments are similar to SPAdes.
-
-Paired reads assembly:
-
- ./gatb -1 read_1.fastq -2 read_2.fastq
-
-paired-end reads given in a single file:
-
- ./gatb --12 interleaved_reads.fastq
-
-Unpaired reads:
-
- ./gatb -s single_reads.fastq
-
-The final assembly is in:
-
- assembly.fasta
-
-All other files are intermediary.
-
-More input options are available. Type `./gatb` for extended usage.
-
-Since the pipeline is multi-k, it is unnecessary to specify a kmer size.
-
-Install FAQ
----
-
-Don't copy the `./gatb` script to a bin folder it is meant to stay in that directory.
-
-If you have trouble installing BESST, just give up and run `./gatb` nevertheless. You can just skip the scaffolding step and the pipeline will still generate contigs.
-
-If you want to persist compiling, read on.
-
-Can't install BESST ? Try [Conda (with Python 2)](https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh) or [Activestate](http://www.activestate.com/activepython/downloads)
-
-Support
--------
-
-To contact an author directly: rayan.chikhi@ens-cachan.org
diff --git a/external/gatb-minia-pipeline/bloocoo/Bloocoo b/external/gatb-minia-pipeline/bloocoo/Bloocoo
deleted file mode 100755
index 285d4610ace2eabd143d2d5037b23dfb576e3846..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/bloocoo/Bloocoo and /dev/null differ
diff --git a/external/gatb-minia-pipeline/bloocoo/README b/external/gatb-minia-pipeline/bloocoo/README
deleted file mode 100644
index 7bdc7d61cdb54791f120a4fe5f3ac6711aebabfa..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/bloocoo/README
+++ /dev/null
@@ -1,14 +0,0 @@
----------------------------------------------------------------------------------------
-History
----------------------------------------------------------------------------------------
-2015/11/25
-Binary Bloocoo build for Linux target (on a IGRIDA 'bermuda' node, cf. OAR snippet below)
-from http://gatb-tools.gforge.inria.fr/versions/src/Bloocoo-1.0.6-Source.tar.gz
-oarsub -I -l /nodes=1,walltime=1 -p "cluster='bermuda'"
----------------------------------------------------------------------------------------
-2015/10/01
-Binary Bloocoo build for Linux target (on igrida01-12)
-from gatb-tools sources http://gatb-tools.gforge.inria.fr/versions/src/Bloocoo-1.0.5-Source.tar.gz
-
-(cf. /udd/cdeltel/bioinfo/anr-gatb/Bloocoo-1.0.5-Source/build)
----------------------------------------------------------------------------------------
diff --git a/external/gatb-minia-pipeline/dependencies/delivery.sh b/external/gatb-minia-pipeline/dependencies/delivery.sh
deleted file mode 120000
index 25f039c7ec6c7292b259a3f58da4803b344df568..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/dependencies/delivery.sh
+++ /dev/null
@@ -1 +0,0 @@
-../../gatb-tools/gatb-tools/thirdparty/gatb-core/gatb-core/scripts/delivery.sh
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-p1-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-p1-igrida.sh
deleted file mode 100755
index ff7ddd1312bd8883c646006d9bd58ea133ef5521..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-p1-igrida.sh
+++ /dev/null
@@ -1,148 +0,0 @@
-#!/bin/bash
-#==============================================================================
-# G A T B P I P E L I N E
-#==============================================================================
-#
-# History
-# 2013-11-18: Change the quast command (contigs were evaluated, instead of scaffolds)
-#
-#==============================================================================
-#
-#------------------------------------------------------------------------------
-# Job parameters
-#------------------------------------------------------------------------------
-#OAR -n gatb-p1
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=20:00:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p1/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p1/outjobs/run.%jobid%.out
-
-# we use IGRIDA the following IGRIDA clusters (see http://igrida.gforge.inria.fr/practices.html)
-# bermuda : 2 x 4 cores Gulftown Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 48GB
-
-
-# TODOs
-# use *local* disk for the run (instead of the NFS dir. /temp_dd/...)
-# make this script more generic (currently only for cdeltel)
-# check the compilation options (O3, openmp, sse, etc.)
-# add md5sum check after transfering the data
-# synthetize results, send report
-
-
-set -xv
-
-
-PIP=p1 # pipeline name
-
-source /udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/gatb-pipeline-common.sh
-
-EXT_print_job_informations
-
-EXT_send_starting_mail
-
-EXT_define_paths
-
-
-#------------------------------------------------------------------------------
-# Prepare the data
-#------------------------------------------------------------------------------
-#rsync -uv genocluster2:$DATA_GENOUEST/*fastq $DATA_IGRIDA/
-
-#for Quast validation
-#rsync -uv genocluster2:/omaha-beach/Assemblathon1/speciesA.diploid.fa $DATA_IGRIDA/
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-
-mkdir -p $PIPELINE
-cd $PIPELINE/
-pwd
-
-EXT_download_source_code
-
-EXT_print_versioning_informations
-
-
-#------------------------------------------------------------------------------
-# Compile the codes
-#------------------------------------------------------------------------------
-cd $PIPELINE/git-gatb-pipeline/
-ln -sf ../specialk kmergenie
-#ln -sf ../superscaffolder superscaffolder
-ln -sf ../debloom minia
-
-make
-MAKE_EXIT_CODE=$?
-
-#------------------------------------------------------------------------------
-# Default simple test
-#------------------------------------------------------------------------------
-#make test
-
-#------------------------------------------------------------------------------
-# Assemblathon-1 benchmark
-#------------------------------------------------------------------------------
-#FASTQ_LIST=`ls $DATA_IGRIDA/*fastq`
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "Check compatibility with the command below:"
-
-mkdir $WORKDIR/run
-cd $WORKDIR/run
-
-date
-START_TIME=`date +"%s"`
-
-#time ls xxx
-
-# P1
-time $MEMUSED $GATB_SCRIPT \
- -p $DATA_IGRIDA/speciesA_200i_40x.1.fastq $DATA_IGRIDA/speciesA_200i_40x.2.fastq \
- -p $DATA_IGRIDA/speciesA_300i_40x.1.fastq $DATA_IGRIDA/speciesA_300i_40x.2.fastq \
- -m $DATA_IGRIDA/speciesA_3000i_20x_r3.1.fastq $DATA_IGRIDA/speciesA_3000i_20x_r3.2.fastq \
- -m $DATA_IGRIDA/speciesA_10000i_20x_r3.1.fastq $DATA_IGRIDA/speciesA_10000i_20x_r3.2.fastq
-
-CMD_EXIT_CODE=$?
-
-END_TIME=`date +"%s"`
-
-(( DURATION_TIME = END_TIME - START_TIME ))
-
-date
-
-EXT_non_regression_update_logbook
-
-
-#------------------------------------------------------------------------------
-# Job summary
-#------------------------------------------------------------------------------
-
-EXT_send_ending_mail
-
-
-#------------------------------------------------------------------------------
-# Synthetize results
-#------------------------------------------------------------------------------
-
-# Validation of the results
-
-outfile=assembly.besst.scaffolds.fasta
-$QUAST_CMD $outfile -R $DATA_IGRIDA/speciesA.diploid.fa --scaffolds --min-contig 100
-
-
-# Non regression tests
-
-EXT_non_regression_execution_time # todo
-
-EXT_non_regression_quast
-
-EXT_non_regression_plot
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-EXT_transfer_reports_to_genouest
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-p2-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-p2-igrida.sh
deleted file mode 100755
index 7445df7cbe01b8965d84b0d6b887f235c87747af..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-p2-igrida.sh
+++ /dev/null
@@ -1,146 +0,0 @@
-#!/bin/bash
-#==============================================================================
-# G A T B P I P E L I N E
-#==============================================================================
-#
-# History
-# 2013-11-18: Change the quast command (contigs were evaluated, instead of scaffolds)
-#
-#==============================================================================
-#
-#------------------------------------------------------------------------------
-# Job parameters
-#------------------------------------------------------------------------------
-#OAR -n gatb-p2
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=20:00:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p2/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p2/outjobs/run.%jobid%.out
-
-# we use IGRIDA the following IGRIDA clusters (see http://igrida.gforge.inria.fr/practices.html)
-# bermuda : 2 x 4 cores Gulftown Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 48GB
-
-
-# TODOs
-# use *local* disk for the run (instead of the NFS dir. /temp_dd/...)
-# make this script more generic (currently only for cdeltel)
-# check the compilation options (O3, openmp, sse, etc.)
-# add md5sum check after transfering the data
-# synthetize results, send report
-
-
-set -xv
-
-
-PIP=p2 # pipeline name
-
-source /udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/gatb-pipeline-common.sh
-
-EXT_print_job_informations
-
-EXT_send_starting_mail
-
-EXT_define_paths
-
-
-#------------------------------------------------------------------------------
-# Prepare the data
-#------------------------------------------------------------------------------
-#rsync -uv genocluster2:$DATA_GENOUEST/*fastq $DATA_IGRIDA/
-
-#for Quast validation
-#rsync -uv genocluster2:/omaha-beach/Assemblathon1/speciesA.diploid.fa $DATA_IGRIDA/
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-
-mkdir -p $PIPELINE
-cd $PIPELINE/
-pwd
-
-EXT_download_source_code
-
-EXT_print_versioning_informations
-
-
-#------------------------------------------------------------------------------
-# Compile the codes
-#------------------------------------------------------------------------------
-cd $PIPELINE/git-gatb-pipeline/
-ln -sf ../specialk kmergenie
-#ln -sf ../superscaffolder superscaffolder
-ln -sf ../debloom minia
-
-make
-MAKE_EXIT_CODE=$?
-
-#------------------------------------------------------------------------------
-# Default simple test
-#------------------------------------------------------------------------------
-#make test
-
-#------------------------------------------------------------------------------
-# Assemblathon-1 benchmark
-#------------------------------------------------------------------------------
-#FASTQ_LIST=`ls $DATA_IGRIDA/*fastq`
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "Check compatibility with the command below:"
-
-mkdir $WORKDIR/run
-cd $WORKDIR/run
-
-date
-START_TIME=`date +"%s"`
-
-#time ls xxx
-
-time $MEMUSED $GATB_SCRIPT \
- -p $DATA_IGRIDA/frag_1.fastq.gz $DATA_IGRIDA/frag_2.fastq.gz \
- -m $DATA_IGRIDA/shortjump_1.fastq.gz $DATA_IGRIDA/shortjump_2.fastq.gz \
- -p $DATA_IGRIDA/longjump_1.fastq.gz $DATA_IGRIDA/longjump_2.fastq.gz
-
-CMD_EXIT_CODE=$?
-
-END_TIME=`date +"%s"`
-
-(( DURATION_TIME = END_TIME - START_TIME ))
-
-date
-
-EXT_non_regression_update_logbook
-
-
-#------------------------------------------------------------------------------
-# Job summary
-#------------------------------------------------------------------------------
-
-EXT_send_ending_mail
-
-
-#------------------------------------------------------------------------------
-# Synthetize results
-#------------------------------------------------------------------------------
-
-# Validation of the results
-
-outfile=assembly.besst.scaffolds.fasta
-$QUAST_CMD $outfile -R $DATA_IGRIDA/genome.fasta --scaffolds --min-contig 100
-
-# Non regression tests
-
-EXT_non_regression_execution_time # todo
-
-EXT_non_regression_quast
-
-EXT_non_regression_plot
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-
-EXT_transfer_reports_to_genouest
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-p3-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-p3-igrida.sh
deleted file mode 100755
index 499da3d825c0feec02abfc5cc7a13634605585e7..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-p3-igrida.sh
+++ /dev/null
@@ -1,148 +0,0 @@
-#!/bin/bash
-#==============================================================================
-# G A T B P I P E L I N E
-#==============================================================================
-#
-# History
-# 2013-11-18: Change the quast command (contigs were evaluated, instead of scaffolds)
-#
-#==============================================================================
-#
-#------------------------------------------------------------------------------
-# Job parameters
-#------------------------------------------------------------------------------
-#OAR -n gatb-p3
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=20:00:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p3/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p3/outjobs/run.%jobid%.out
-
-# we use IGRIDA the following IGRIDA clusters (see http://igrida.gforge.inria.fr/practices.html)
-# bermuda : 2 x 4 cores Gulftown Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 48GB
-
-
-# TODOs
-# use *local* disk for the run (instead of the NFS dir. /temp_dd/...)
-# make this script more generic (currently only for cdeltel)
-# check the compilation options (O3, openmp, sse, etc.)
-# add md5sum check after transfering the data
-# synthetize results, send report
-
-
-set -xv
-
-
-PIP=p3 # pipeline name
-
-source /udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/gatb-pipeline-common.sh
-
-EXT_print_job_informations
-
-EXT_send_starting_mail
-
-EXT_define_paths
-
-###if [ 1 -eq 0 ]; then
-
-#------------------------------------------------------------------------------
-# Prepare the data
-#------------------------------------------------------------------------------
-#rsync -uv genocluster2:$DATA_GENOUEST/*fastq $DATA_IGRIDA/
-
-#for Quast validation
-#rsync -uv genocluster2:/omaha-beach/Assemblathon1/speciesA.diploid.fa $DATA_IGRIDA/
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-
-mkdir -p $PIPELINE
-cd $PIPELINE/
-pwd
-
-EXT_download_source_code
-
-EXT_print_versioning_informations
-
-
-#------------------------------------------------------------------------------
-# Compile the codes
-#------------------------------------------------------------------------------
-cd $PIPELINE/git-gatb-pipeline/
-ln -sf ../specialk kmergenie
-#ln -sf ../superscaffolder superscaffolder
-ln -sf ../debloom minia
-
-make
-MAKE_EXIT_CODE=$?
-
-#------------------------------------------------------------------------------
-# Default simple test
-#------------------------------------------------------------------------------
-#make test
-
-#------------------------------------------------------------------------------
-# Assemblathon-1 benchmark
-#------------------------------------------------------------------------------
-#FASTQ_LIST=`ls $DATA_IGRIDA/*fastq`
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "Check compatibility with the command below:"
-
-mkdir $WORKDIR/run
-cd $WORKDIR/run
-
-date
-START_TIME=`date +"%s"`
-
-#time ls xxx
-
-time $MEMUSED $GATB_SCRIPT \
- -p $DATA_IGRIDA/frag_1.fastq $DATA_IGRIDA/frag_2.fastq \
- -p $DATA_IGRIDA/shortjump_1.fastq $DATA_IGRIDA/shortjump_2.fastq
-
-CMD_EXIT_CODE=$?
-
-END_TIME=`date +"%s"`
-
-(( DURATION_TIME = END_TIME - START_TIME ))
-
-date
-
-EXT_non_regression_update_logbook
-
-
-#------------------------------------------------------------------------------
-# Job summary
-#------------------------------------------------------------------------------
-
-EXT_send_ending_mail
-
-
-#------------------------------------------------------------------------------
-# Synthetize results
-#------------------------------------------------------------------------------
-
-# Validation of the results
-
-outfile=assembly.besst.scaffolds.fasta
-$QUAST_CMD $outfile -R $DATA_IGRIDA/genome.fasta --scaffolds --min-contig 100
-
-
-# Non regression tests
-
-EXT_non_regression_execution_time # todo
-
-EXT_non_regression_quast
-
-###fi
-
-EXT_non_regression_plot
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-EXT_transfer_reports_to_genouest
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-p4-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-p4-igrida.sh
deleted file mode 100755
index bba0e0f9e1d88098271df51f65c7b46f0e2f7b3b..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-p4-igrida.sh
+++ /dev/null
@@ -1,144 +0,0 @@
-#!/bin/bash
-#==============================================================================
-# G A T B P I P E L I N E
-#==============================================================================
-#
-# History
-# 2013-11-18: Change the quast command (contigs were evaluated, instead of scaffolds)
-#
-#==============================================================================
-#
-#------------------------------------------------------------------------------
-# Job parameters
-#------------------------------------------------------------------------------
-#OAR -n gatb-p4
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=00:30:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p4/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p4/outjobs/run.%jobid%.out
-
-# we use IGRIDA the following IGRIDA clusters (see http://igrida.gforge.inria.fr/practices.html)
-# bermuda : 2 x 4 cores Gulftown Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 48GB
-
-
-# TODOs
-# use *local* disk for the run (instead of the NFS dir. /temp_dd/...)
-# make this script more generic (currently only for cdeltel)
-# check the compilation options (O3, openmp, sse, etc.)
-# add md5sum check after transfering the data
-# synthetize results, send report
-
-
-set -xv
-
-
-PIP=p4 # pipeline name
-
-source /udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/gatb-pipeline-common.sh
-
-EXT_print_job_informations
-
-EXT_send_starting_mail
-
-EXT_define_paths
-
-
-#------------------------------------------------------------------------------
-# Prepare the data
-#------------------------------------------------------------------------------
-#rsync -uv genocluster2:$DATA_GENOUEST/*fastq $DATA_IGRIDA/
-
-#for Quast validation
-#rsync -uv genocluster2:/omaha-beach/Assemblathon1/speciesA.diploid.fa $DATA_IGRIDA/
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-
-mkdir -p $PIPELINE
-cd $PIPELINE/
-pwd
-
-EXT_download_source_code
-
-EXT_print_versioning_informations
-
-
-#------------------------------------------------------------------------------
-# Compile the codes
-#------------------------------------------------------------------------------
-cd $PIPELINE/git-gatb-pipeline/
-ln -sf ../specialk kmergenie
-#ln -sf ../superscaffolder superscaffolder
-ln -sf ../debloom minia
-
-make
-MAKE_EXIT_CODE=$?
-
-#------------------------------------------------------------------------------
-# Default simple test
-#------------------------------------------------------------------------------
-#make test
-
-#------------------------------------------------------------------------------
-# Assemblathon-1 benchmark
-#------------------------------------------------------------------------------
-#FASTQ_LIST=`ls $DATA_IGRIDA/*fastq`
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "Check compatibility with the command below:"
-
-mkdir $WORKDIR/run
-cd $WORKDIR/run
-
-date
-START_TIME=`date +"%s"`
-
-#time ls xxx
-
-time $MEMUSED $GATB_SCRIPT \
- -p $DATA_IGRIDA/frag_1.fastq $DATA_IGRIDA/frag_2.fastq \
- -p $DATA_IGRIDA/shortjump_1.fastq $DATA_IGRIDA/shortjump_2.fastq
-
-CMD_EXIT_CODE=$?
-
-END_TIME=`date +"%s"`
-
-(( DURATION_TIME = END_TIME - START_TIME ))
-
-date
-
-EXT_non_regression_update_logbook
-
-
-#------------------------------------------------------------------------------
-# Job summary
-#------------------------------------------------------------------------------
-
-EXT_send_ending_mail
-
-
-#------------------------------------------------------------------------------
-# Synthetize results
-#------------------------------------------------------------------------------
-
-# Validation of the results
-
-outfile=assembly.besst.scaffolds.fasta
-$QUAST_CMD $outfile -R $DATA_IGRIDA/genome.fasta --scaffolds --min-contig 100
-
-# Non regression tests
-
-EXT_non_regression_execution_time # todo
-
-EXT_non_regression_quast
-
-EXT_non_regression_plot
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-EXT_transfer_reports_to_genouest
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-p5-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-p5-igrida.sh
deleted file mode 100755
index bd347ff9d84a511fa54d556113b7a56d8c6167d8..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-p5-igrida.sh
+++ /dev/null
@@ -1,147 +0,0 @@
-#!/bin/bash
-#==============================================================================
-# G A T B P I P E L I N E
-#==============================================================================
-#
-# History
-# 2013-11-18: Change the quast command (contigs were evaluated, instead of scaffolds)
-#
-#==============================================================================
-#
-#------------------------------------------------------------------------------
-# Job parameters
-#------------------------------------------------------------------------------
-#OAR -n gatb-p5
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=160:00:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p5/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p5/outjobs/run.%jobid%.out
-
-# we use IGRIDA the following IGRIDA clusters (see http://igrida.gforge.inria.fr/practices.html)
-# bermuda : 2 x 4 cores Gulftown Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 48GB
-
-
-# TODOs
-# use *local* disk for the run (instead of the NFS dir. /temp_dd/...)
-# make this script more generic (currently only for cdeltel)
-# check the compilation options (O3, openmp, sse, etc.)
-# add md5sum check after transfering the data
-# synthetize results, send report
-
-
-set -xv
-
-
-PIP=p5 # pipeline name
-
-source /udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/gatb-pipeline-common.sh
-
-EXT_print_job_informations
-
-EXT_send_starting_mail
-
-EXT_define_paths
-
-
-#------------------------------------------------------------------------------
-# Prepare the data
-#------------------------------------------------------------------------------
-#rsync -uv genocluster2:$DATA_GENOUEST/*fastq $DATA_IGRIDA/
-
-#for Quast validation
-#rsync -uv genocluster2:/omaha-beach/Assemblathon1/speciesA.diploid.fa $DATA_IGRIDA/
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-
-mkdir -p $PIPELINE
-cd $PIPELINE/
-pwd
-
-EXT_download_source_code
-
-EXT_print_versioning_informations
-
-
-#------------------------------------------------------------------------------
-# Compile the codes
-#------------------------------------------------------------------------------
-cd $PIPELINE/git-gatb-pipeline/
-ln -sf ../specialk kmergenie
-#ln -sf ../superscaffolder superscaffolder
-ln -sf ../debloom minia
-
-make
-MAKE_EXIT_CODE=$?
-
-#------------------------------------------------------------------------------
-# Default simple test
-#------------------------------------------------------------------------------
-#make test
-
-#------------------------------------------------------------------------------
-# Assemblathon-1 benchmark
-#------------------------------------------------------------------------------
-#FASTQ_LIST=`ls $DATA_IGRIDA/*fastq`
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "Check compatibility with the command below:"
-
-mkdir $WORKDIR/run
-cd $WORKDIR/run
-
-date
-START_TIME=`date +"%s"`
-
-#time ls xxx
-
-time $MEMUSED $GATB_SCRIPT \
- -p $DATA_IGRIDA/frag_1.fastq.gz $DATA_IGRIDA/frag_2.fastq.gz \
- -p $DATA_IGRIDA/shortjump_1.fastq.gz $DATA_IGRIDA/shortjump_2.fastq.gz \
- -p $DATA_IGRIDA/mediumjump_1.fastq.gz $DATA_IGRIDA/mediumjump_2.fastq.gz
-
-
-CMD_EXIT_CODE=$?
-
-END_TIME=`date +"%s"`
-
-(( DURATION_TIME = END_TIME - START_TIME ))
-
-date
-
-EXT_non_regression_update_logbook
-
-
-#------------------------------------------------------------------------------
-# Job summary
-#------------------------------------------------------------------------------
-
-EXT_send_ending_mail
-
-
-#------------------------------------------------------------------------------
-# Synthetize results
-#------------------------------------------------------------------------------
-
-# Validation of the results
-
-outfile=assembly.besst.scaffolds.fasta
-$QUAST_CMD $outfile --scaffolds --min-contig 100
-
-
-# Non regression tests
-
-EXT_non_regression_execution_time # todo
-
-EXT_non_regression_quast
-
-EXT_non_regression_plot
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-EXT_transfer_reports_to_genouest
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-p6-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-p6-igrida.sh
deleted file mode 100755
index 5d351aa87e1f6a5a6b62563dcbc4cf4eb6f75e4b..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-p6-igrida.sh
+++ /dev/null
@@ -1,150 +0,0 @@
-#!/bin/bash
-#==============================================================================
-# G A T B P I P E L I N E
-#==============================================================================
-#
-# History
-# 2013-11-18: Change the quast command (contigs were evaluated, instead of scaffolds)
-#
-#==============================================================================
-#
-#------------------------------------------------------------------------------
-# Job parameters
-#------------------------------------------------------------------------------
-#OAR -n gatb-p6
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=160:00:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p6/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p6/outjobs/run.%jobid%.out
-
-# we use IGRIDA the following IGRIDA clusters (see http://igrida.gforge.inria.fr/practices.html)
-# bermuda : 2 x 4 cores Gulftown Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 48GB
-
-
-# TODOs
-# use *local* disk for the run (instead of the NFS dir. /temp_dd/...)
-# make this script more generic (currently only for cdeltel)
-# check the compilation options (O3, openmp, sse, etc.)
-# add md5sum check after transfering the data
-# synthetize results, send report
-
-
-set -xv
-
-
-PIP=p6 # pipeline name
-
-source /udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/gatb-pipeline-common.sh
-
-EXT_print_job_informations
-
-EXT_send_starting_mail
-
-EXT_define_paths
-
-
-#------------------------------------------------------------------------------
-# Prepare the data
-#------------------------------------------------------------------------------
-#rsync -uv genocluster2:$DATA_GENOUEST/*fastq $DATA_IGRIDA/
-
-#for Quast validation
-#rsync -uv genocluster2:/omaha-beach/Assemblathon1/speciesA.diploid.fa $DATA_IGRIDA/
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-
-mkdir -p $PIPELINE
-cd $PIPELINE/
-pwd
-
-EXT_download_source_code
-
-EXT_print_versioning_informations
-
-
-#------------------------------------------------------------------------------
-# Compile the codes
-#------------------------------------------------------------------------------
-cd $PIPELINE/git-gatb-pipeline/
-ln -sf ../specialk kmergenie
-#ln -sf ../superscaffolder superscaffolder
-ln -sf ../debloom minia
-
-make
-MAKE_EXIT_CODE=$?
-
-#------------------------------------------------------------------------------
-# Default simple test
-#------------------------------------------------------------------------------
-#make test
-
-#------------------------------------------------------------------------------
-# Assemblathon-1 benchmark
-#------------------------------------------------------------------------------
-#FASTQ_LIST=`ls $DATA_IGRIDA/*fastq`
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "Check compatibility with the command below:"
-
-mkdir $WORKDIR/run
-cd $WORKDIR/run
-
-date
-START_TIME=`date +"%s"`
-
-#time ls xxx
-
-time $MEMUSED $GATB_SCRIPT \
- -p $DATA_IGRIDA/625E1AAXX.1_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.1_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.2_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.2_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.3_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.3_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.4_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.4_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.5_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.5_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.6_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.6_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.7_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.7_trim2.fastq.gz \
- -p $DATA_IGRIDA/625E1AAXX.8_trim1.fastq.gz $DATA_IGRIDA/625E1AAXX.8_trim2.fastq.gz
-
-CMD_EXIT_CODE=$?
-
-END_TIME=`date +"%s"`
-
-(( DURATION_TIME = END_TIME - START_TIME ))
-
-date
-
-EXT_non_regression_update_logbook
-
-
-#------------------------------------------------------------------------------
-# Job summary
-#------------------------------------------------------------------------------
-
-EXT_send_ending_mail
-
-
-#------------------------------------------------------------------------------
-# Synthetize results
-#------------------------------------------------------------------------------
-
-# Validation of the results
-
-outfile=assembly.besst.scaffolds.fasta
-$QUAST_CMD $outfile --scaffolds --min-contig 100
-
-# Non regression tests
-
-EXT_non_regression_execution_time # todo
-
-EXT_non_regression_quast
-
-EXT_non_regression_plot
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-EXT_transfer_reports_to_genouest
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-pipeline-common.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-pipeline-common.sh
deleted file mode 100755
index eb33920f892d23deaba26ad5b2f7a5bf58ecca8c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-pipeline-common.sh
+++ /dev/null
@@ -1,260 +0,0 @@
-#!/bin/bash
-
-echo
-echo "Sourcing gatb-pipeline-common.sh ..."
-echo
-
-PATH="/udd/cdeltel/bioinfo/bwa-0.7.10/:.:$PATH"
-PATH="/udd/cdeltel/bioinfo/seqtk/:.:$PATH"
-
-MAIL_DST_ALL_MESG=charles.deltel@inria.fr
-MAIL_DST_ERR_ONLY="cdeltel@laposte.net rchikhi@gmail.com"
-
-MAIL_CMD="ssh igrida-oar-frontend mail "
-
-#LOGBOOK=/udd/cdeltel/bioinfo/anr-gatb/logbook-${PIP}.txt => Currently read-only file system!
-LOGBOOK_ROOT=logbook-${PIP}
-LOGBOOK_TXT=/temp_dd/igrida-fs1/cdeltel/bioinfo/${LOGBOOK_ROOT}.txt
-LOGBOOK_POS=/temp_dd/igrida-fs1/cdeltel/bioinfo/${LOGBOOK_ROOT}.ps
-
-TODAY=`date +'%Y/%m/%d'`
-
-#------------------------------------------------------------------------------
-# Data paths
-#------------------------------------------------------------------------------
-DATA_GENOUEST=
-
-case "$PIP" in
- p1) DATA_NAME=Assemblathon1/data ;;
- p2) DATA_NAME=chr14-gage ;;
- p3) DATA_NAME=Staphylococcus_aureus/Data/original ;;
- p4) DATA_NAME=Rhodobacter_sphaeroides/Data/original ;;
- p5) DATA_NAME=Bombus_impatiens/Data/original ;; # données à vérifier ???
- p6) DATA_NAME=Assemblathon2/fish/fastq ;;
- *) echo Error; exit 1; ;;
-esac
-
-DATA_IGRIDA=/temp_dd/igrida-fs1/cdeltel/bioinfo/${DATA_NAME}/
-REPORTS_GENOUEST=/home/symbiose/cdeltel/anr-gatb/reports/igrida/gatb-${PIP}/
-
-#------------------------------------------------------------------------------
-# Host infos
-#------------------------------------------------------------------------------
-lstopo --of txt
-
-#------------------------------------------------------------------------------
-# Tools
-#------------------------------------------------------------------------------
-duration() {
- local dt=${1}
- ((h=dt/3600))
- ((m=dt%3600/60))
- ((s=dt%60))
- printf "%03dh:%02dm:%0ds\n" $h $m $s
-}
-
-#------------------------------------------------------------------------------
-# Job infos
-#------------------------------------------------------------------------------
-EXT_print_job_informations() {
- echo "hostname : " `hostname`
- echo "TODAY : $TODAY"
- echo "OAR_JOB_NAME : $OAR_JOB_NAME"
- echo "OAR_JOB_ID : $OAR_JOB_ID"
- echo "OAR_ARRAY_ID : $OAR_ARRAY_ID"
- echo "OAR_ARRAY_INDEX : $OAR_ARRAY_INDEX"
-}
-
-EXT_send_starting_mail() {
- SUBJECT="[gatb-${PIP}]-job$OAR_JOB_ID-starts"
- $MAIL_CMD $MAIL_DST_ALL_MESG -s "$SUBJECT" << EOF
-OAR_JOB_ID: $OAR_JOB_ID - hostname: `hostname`
-EOF
-}
-
-#------------------------------------------------------------------------------
-# Send an e-mail when job starts/ends
-#------------------------------------------------------------------------------
-EXT_send_ending_mail() {
- echo "JOB_SUMMARY"
- SUBJECT="[gatb-${PIP}]-job$OAR_JOB_ID-ends-`duration $DURATION_TIME`"
- $MAIL_CMD $MAIL_DST_ALL_MESG -s "$SUBJECT" << EOF
-$JOB_SUMMARY
-EOF
- if [ $CMD_EXIT_CODE -ne 0 ] || [ $MAKE_EXIT_CODE -ne 0 ]; then
- SUBJECT="[gatb-${PIP}]-job$OAR_JOB_ID-ends-Error"
- $MAIL_CMD $MAIL_DST_ALL_MESG $MAIL_DST_ERR_ONLY -s "$SUBJECT" << EOF
-This is to inform you that the GATB ${PIP} pipeline exited with error:
- MAKE_EXIT_CODE: $MAKE_EXIT_CODE
- CMD_EXIT_CODE: $CMD_EXIT_CODE
-EOF
- fi
-}
-
-#------------------------------------------------------------------------------
-# Download the code
-#------------------------------------------------------------------------------
-EXT_download_source_code() {
- git clone git+ssh://cdeltel@scm.gforge.inria.fr//gitroot/gatb-pipeline/gatb-pipeline.git git-gatb-pipeline
- [ $? -ne 0 ] && { echo "git clone error"; exit 1;}
- cd git-gatb-pipeline
- git submodule init
- git submodule update
- [ $? -ne 0 ] && { echo "git submodule error"; exit 1;}
- git submodule status
- cd ..
- svn co svn+ssh://scm.gforge.inria.fr/svnroot/projetssymbiose/superscaffolder superscaffolder
- [ $? -ne 0 ] && { echo "svn co error"; exit 1;}
- svn co svn+ssh://scm.gforge.inria.fr/svnroot/projetssymbiose/minia/trunk debloom
- [ $? -ne 0 ] && { echo "svn co error"; exit 1;}
- svn co svn+ssh://scm.gforge.inria.fr/svnroot/projetssymbiose/specialk specialk
- [ $? -ne 0 ] && { echo "svn co error"; exit 1;}
-}
-
-#------------------------------------------------------------------------------
-# Code versioning informations
-#------------------------------------------------------------------------------
-EXT_print_versioning_informations() {
- INFOS_GATB_PIPELINE=$PIPELINE/git-gatb-infos.txt
- INFOS_SUPERSCAFFOLDER=$PIPELINE/svn-superscaffolder-infos.txt
- INFOS_DEBLOOM=$PIPELINE/svn-debloom-infos.txt
- INFOS_SPECIALK=$PIPELINE/svn-specialk-infos.txt
-
- #..............................................................................
- cd $PIPELINE/git-gatb-pipeline
- git log --max-count=1 > $INFOS_GATB_PIPELINE
- cat $INFOS_GATB_PIPELINE
- #..............................................................................
- cd $PIPELINE/superscaffolder
- svn info > $INFOS_SUPERSCAFFOLDER
- svn log --limit 10 >> $INFOS_SUPERSCAFFOLDER
- cat $INFOS_SUPERSCAFFOLDER
- #..............................................................................
- cd $PIPELINE/specialk
- svn info > $INFOS_SPECIALK
- svn log --limit 10 >> $INFOS_SPECIALK
- cat $INFOS_SPECIALK
- #..............................................................................
- cd $PIPELINE/debloom
- svn info > $INFOS_DEBLOOM
- svn log --limit 10 >> $INFOS_DEBLOOM
- cat $INFOS_DEBLOOM
- #..............................................................................
-}
-
-#------------------------------------------------------------------------------
-# Define where the run will take place
-#------------------------------------------------------------------------------
-EXT_define_paths() {
- #NOW=$(date +"%Y-%m-%d-%H:%M:%S")
-
- #WORKDIR=/temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/p2/2013-07-29-17:50:29
- WORKDIR=/temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/${PIP}/$OAR_JOB_ID
-
- PIPELINE=$WORKDIR/gatb-pipeline
- GATB_SCRIPT=$PIPELINE/git-gatb-pipeline/gatb
- MEMUSED=$PIPELINE/git-gatb-pipeline/tools/memused
- chmod a+x $MEMUSED
- QUAST_PATH=/udd/cdeltel/bioinfo/quast-2.2/
- QUAST_CMD="python $QUAST_PATH/quast.py "
-}
-
-
-#------------------------------------------------------------------------------
-# Non regression tests
-#------------------------------------------------------------------------------
-
-
-EXT_non_regression_update_logbook(){
- OAR_JOB_ID_PREVIOUS="`tail -1 $LOGBOOK|awk '{print $2}'`"
- START_TIME_PREVIOUS="`tail -1 $LOGBOOK|awk '{print $8}'`"
- END_TIME_PREVIOUS="`tail -1 $LOGBOOK|awk '{print $11}'`"
-
- (( DURATION_TIME_PREVIOUS = END_TIME_PREVIOUS - START_TIME_PREVIOUS ))
- (( DT_WITH_PREVIOUS = DURATION_TIME - DURATION_TIME_PREVIOUS ))
-
- JOB_SUMMARY="TODAY: $TODAY - OAR_JOB_ID: $OAR_JOB_ID - hostname: `hostname` - START_TIME: $START_TIME - END_TIME: $END_TIME - DURATION: `duration $DURATION_TIME` - CMD_EXIT_CODE: $CMD_EXIT_CODE - DT_WITH_PREVIOUS: $DT_WITH_PREVIOUS"
- echo "$JOB_SUMMARY" >> $LOGBOOK_TXT
-}
-
-EXT_non_regression_quast() {
- echo "EXT_non_regression_quast: Not ready"
-
- quast_latest=$WORKDIR/../$OAR_JOB_ID_PREVIOUS/run/quast_results/latest/quast.log
- quast_current=$WORKDIR/run/quast_results/latest/quast.log
-
- echo
- echo We compare $quast_latest and $quast_current
- echo
-
- diff $quast_latest $quast_current
-
- echo
-
- if [ $? -ne 0 ]; then
- echo
- echo "WARNING: Quast results differ from previous run!"
- echo
- fi
-}
-
-EXT_non_regression_execution_time() {
- echo "EXT_non_regression_execution_time: TODO"
-}
-
-EXT_non_regression_plot() {
- echo "EXT_non_regression_plot: "
- pwd
-
- awk '{ print $2 }' $LOGBOOK_TXT > c0
- awk '{ print $17 }' $LOGBOOK_TXT |cut -c1-3 > c1
- awk '{ print $17 }' $LOGBOOK_TXT |cut -c6-7 > c2
- awk '{ print $17 }' $LOGBOOK_TXT |cut -c10-|cut -ds -f1 > c3
- paste c0 c1 c2 c3 > tmp
-
- awk '{ printf("%10.2f\n", $2+$3/60.+$4/60./60.) }' tmp > in_hours
- awk '{ printf("%10.2f\n", ($2+$3/60.+$4/60./60.)*60.) }' tmp > in_minutes
-
- paste tmp in_hours in_minutes > ${LOGBOOK_ROOT}_processed.txt
-
- rm -f c0 c1 c2 c3 tmp in_hours in_minutes
-
- COLUMN_HOURS=5
- COLUMN_MINUT=6
-
- case "$PIP" in
- p1) COL=$COLUMN_HOURS ; UNITS="hours";;
- p2) COL=$COLUMN_HOURS ; UNITS="hours";;
- p3) COL=$COLUMN_MINUT ; UNITS="minutes";;
- p4) COL=$COLUMN_MINUT ; UNITS="minutes";;
- p5) COL=$COLUMN_HOURS ; UNITS="hours";;
- p6) COL=$COLUMN_HOURS ; UNITS="hours";;
- *) echo Error; exit 1; ;;
- esac
-
- gnuplot << EOF
-set terminal postscript
-set output "$LOGBOOK_POS"
-set grid
-plot "${LOGBOOK_ROOT}_processed.txt" u $COL w boxes title "${LOGBOOK_ROOT} (in $UNITS)"
-EOF
-
-}
-
-#------------------------------------------------------------------------------
-# Upload run reports to Genouest
-#------------------------------------------------------------------------------
-
-EXT_transfer_reports_to_genouest() {
-
- ssh genocluster2 mkdir -p $REPORTS_GENOUEST/outjobs
- ssh genocluster2 mkdir -p $REPORTS_GENOUEST/quast
-
- rsync -uv $WORKDIR/../outjobs/* genocluster2:$REPORTS_GENOUEST/outjobs/
- rsync -uv $WORKDIR/run/quast_results/results_*/report.txt genocluster2:$REPORTS_GENOUEST/quast/report.$OAR_JOB_ID.txt
-
- rsync -uv $LOGBOOK_TXT genocluster2:$REPORTS_GENOUEST/outjobs/${LOGBOOK_ROOT}.txt
- rsync -uv $LOGBOOK_POS genocluster2:$REPORTS_GENOUEST/outjobs/${LOGBOOK_ROOT}.ps
-
-}
-
diff --git a/external/gatb-minia-pipeline/developer-scripts/gatb-test-igrida.sh b/external/gatb-minia-pipeline/developer-scripts/gatb-test-igrida.sh
deleted file mode 100755
index f853756f2d4fe3feed686e9cf63edcc4adb6c526..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/gatb-test-igrida.sh
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/bin/bash
-# short test (~ 10 minutes)
-#OAR -n gatb-test
-#OAR -p dedicated='none'
-#OAR -l {cluster='bermuda'}/nodes=1,walltime=00:15:00
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/test/outjobs/run.%jobid%.out
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/gatb-pipeline-runs/test/outjobs/run.%jobid%.out
-
-## snippet for manually testing Bloocoo on the dataset used in this script
-## oarsub -I -l /nodes=1,walltime=5 -p "cluster='bermuda'"
-## cd /temp_dd/igrida-fs1/$USER/bioinfo/gatb-pipeline-runs/test/run
-## BLOOCOO=/udd/cdeltel/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/bloocoo/Bloocoo
-## $BLOOCOO -file assembly.list_reads -out tmp.x -abundance-min 2 -kmer-size 31 -nb-cores 8 -slow -high-precision
-
-# =================== job informations =========================================
-echo "hostname : " `hostname`
-echo "TODAY : $TODAY"
-echo "OAR_JOB_NAME : $OAR_JOB_NAME"
-echo "OAR_JOB_ID : $OAR_JOB_ID"
-echo "OAR_ARRAY_ID : $OAR_ARRAY_ID"
-echo "OAR_ARRAY_INDEX : $OAR_ARRAY_INDEX"
-
-FRONTEND=igrida-oar-frontend
-TO=charles.deltel
-ssh $FRONTEND mail $TO@inria.fr -s start_scm_$OAR_JOB_ID << eom
-OAR_JOB_ID: $OAR_JOB_ID - hostname: `hostname`
-eom
-
-TEMP_DD=/temp_dd/igrida-fs1/cdeltel
-RUNDIR=$TEMP_DD/bioinfo/gatb-pipeline-runs/test/run
-LOCKFILE=$TEMP_DD/bioinfo/.gatb-test-lockfile # if exists, only 1 line with $OAR_JOB_ID
-
-# if a similar job is already running, we must kill it before
-echo
-if [ -f $LOCKFILE ]; then
- ssh $FRONTEND oardel `cat $LOCKFILE`
- while true; do
- ssh $FRONTEND oarstat -sj `cat $LOCKFILE` |grep -E 'Terminated|Error' >/dev/null
- [ $? -eq 0 ] && { break; } || { printf "."; sleep 2; }
- done
- rm -f $LOCKFILE
-fi
-echo
-
-echo $OAR_JOB_ID > $LOCKFILE
-
-[ -d $RUNDIR ] || { mkdir $RUNDIR; } && { rm -rf $RUNDIR/*; }
-
-GITDIR=~/bioinfo/anr-gatb/gatb-pipeline/git-gatb-pipeline/
-
-set -xv
-
-cd $GITDIR
-
-# BESST
-git submodule init
-git submodule update
-git submodule status
-
-# superscaffolder => now we use BESST instead
-# cd ../superscaffolder
-# svn update
-
-# minia => currently use the pre-compiled binary file (see minia/minia*)
-# ln -sf ../debloom minia
-# cd ../debloom/
-# svn update
-
-# bwa
-PATH="/udd/cdeltel/bioinfo/bwa-0.7.10/:.:$PATH"
-
-# ================= default very short test ====================================
-cd $GITDIR/test
-../gatb --12 small_test_reads.fa.gz
-echo END_OF_VERY_SHORT_TEST
-
-# ================= short pipeline test (p3) ===================================
-DATA_NAME=Staphylococcus_aureus/Data/original # this is pipeline p3
-DATA_IGRIDA=/temp_dd/igrida-fs1/cdeltel/bioinfo/${DATA_NAME}/
-
-FASTQ_LIST=`ls $DATA_IGRIDA/*fastq*` # gzip
-
-echo "FASTQ list : $FASTQ_LIST"
-echo "(check compatibility with the command below)"
-
-cd $RUNDIR
-
-MEMUSED=$GITDIR/tools/memused
-GATB_SCRIPT=$GITDIR/gatb
-
-time $MEMUSED $GATB_SCRIPT \
- -1 $DATA_IGRIDA/frag_1.fastq -2 $DATA_IGRIDA/frag_2.fastq \
- -1 $DATA_IGRIDA/shortjump_1.fastq -2 $DATA_IGRIDA/shortjump_2.fastq
-
-echo END_OF_SHORT_TEST
-
-ssh $FRONTEND mail $TO@inria.fr -s end_scm_$OAR_JOB_ID << eom
-OAR_JOB_ID: $OAR_JOB_ID - hostname: `hostname`
-
-Get more details with:
-oarstat -fj $OAR_JOB_ID
-eom
diff --git a/external/gatb-minia-pipeline/developer-scripts/test-pipeline-restart.sh b/external/gatb-minia-pipeline/developer-scripts/test-pipeline-restart.sh
deleted file mode 100755
index 71d73e6a086862692cbca0835a9e5aa8389a34b3..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/developer-scripts/test-pipeline-restart.sh
+++ /dev/null
@@ -1,381 +0,0 @@
-#!/bin/bash
-#OAR -n test-pipeline-restart
-#OAR -l /nodes=1,walltime=1:00:00
-##OAR -p cluster='lambda'
-#OAR -p host='igrida12-01.irisa.fr'
-#OAR -O /temp_dd/igrida-fs1/cdeltel/bioinfo/outjobs/test-pipeline-restart.%jobid%.output
-#OAR -E /temp_dd/igrida-fs1/cdeltel/bioinfo/outjobs/test-pipeline-restart.%jobid%.output
-#
-# Cf. redmine gatb-pipeline issue 54
-#
-# Example commands:
-# ./test-pipeline-restart.sh &> output.$(date +%F_%R).log
-# oarsub -S ./test-pipeline-restart.sh
-# To check results: grep "=>" in test-pipeline-restart.%jobid%.output
-
-echo "
------------------------------------------------------------
- Some tests to check gatb-pipeline restartability
- either on error, or to resume minia iterations (on k)
------------------------------------------------------------"
-
-[ -z "$OAR_JOBID" ] && { myecho "Error, this script must be launched inside a job"; exit 1; }
-
-init_env() {
- # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> edit me >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
- export GATB_dir=/udd/cdeltel/gatb/gatb-pipeline
- export DATADIR=$GATB_dir/gatb-web-test-data
- export GATB_script=$GATB_dir/git-gatb-pipeline/gatb
- export BWA_PATH=/udd/cdeltel/bioinfo/bwa-0.7.10
-
- USE_CASE=1
- case $USE_CASE in
- 1)
- export WORKDIR=/temp_dd/igrida-fs1/cdeltel/workdir-test-pipeline-restart-1file
- export DATA_OPTIONS="-s $DATADIR/small_test_reads.fa.gz"
- ;;
- 2)
- export WORKDIR=/temp_dd/igrida-fs1/cdeltel/workdir-test-pipeline-restart-2files
- export DATA_OPTIONS="-1 $DATADIR/SRR959239_1_small_100Klines.fastq.gz -2 $DATADIR/SRR959239_2_small_100Klines.fastq.gz"
- ;;
- *)
- myecho "Error in USE_CASE"
- exit
- ;;
- esac
- myecho "Pipeline data options : $DATA_OPTIONS"
-
- [ -d $WORKDIR ] && { myecho "Cleaning $WORKDIR..."; rm -rf $WORKDIR; }
- export PATH="$BWA_PATH:$PATH"
-
- # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-}
-
-myecho () { echo "=> $*"; }
-
-########################################################################################
-# 1. Without Bloocoo (use --no-error-correction)
-########################################################################################
-
-#---------------------------------------------------------------------------------------
-# 1.1 Runs without bloocoo, without restart: ref. results, repeat to check reproductibility
-#---------------------------------------------------------------------------------------
-
-without_bloocoo_reference () {
- [ -z $1 ] && { echo " Missing argument"; exit; }
-
- #-- minia single-threaded, no bloocoo
- myecho "without_bloocoo_reference : reference run..."
- WORKDIR_subdir=without_bloocoo_debug_mode_1
- for runId in $reproductibility_iterations; do
- TMPDIR=$WORKDIR/$WORKDIR_subdir/run-$runId
- mkdir -p $TMPDIR && cd $TMPDIR
- [ "$1" = "YES" ] && { time $GATB_script --debug 1 --no-error-correction $DATA_OPTIONS; } || { myecho "no run"; }
- eval export ASB_REF_without_bloocoo_debug_mode_1_run${runId}=$TMPDIR/assembly.fasta
- done
-}
-
-#---------------------------------------------------------------------------------------
-# 1.2 Runs without bloocoo, with restart ON ERROR
-#---------------------------------------------------------------------------------------
-without_bloocoo_restart_on_error () {
- [ -z $1 ] && { myecho " Missing argument"; exit; }
-
- TMPDIR=$WORKDIR/without_bloocoo_debug_mode_1_restart_on_error/run-1
- export ASB_without_bloocoo_restart_on_error_run1=$TMPDIR/assembly.fasta
-
- myecho "without_bloocoo_restart_on_error"
- if [ "$1" != "YES" ]; then # only useful to recall ABS_ env. variable
- myecho "no run"
-
- else
- [ -d $TMPDIR ] && { myecho "Cleaning $TMPDIR..."; rm -rf $TMPDIR; }
- mkdir -p $TMPDIR && cd $TMPDIR
-
- #-- step 1 : emulate an error
- myecho "without_bloocoo_restart_on_error : emulate an error..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 --no-error-correction $DATA_OPTIONS &
- #############################################################
-
- pid=$! && touch step1.pid$pid.started
- WATCH_FILE=assembly.list_reads.41
- while [ ! -f $WATCH_FILE ]; do sleep 2; done
-
- touch step1.pid$pid.killed
- killall python memused minia
-
- myecho "without_bloocoo_restart_on_error continue"
- sleep 5
-
- #-- step 2 : resume interrupted simulation (restart on error)
- myecho "without_bloocoo_restart_on_error : resume interrupted simulation (restart on error)..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 --no-error-correction $DATA_OPTIONS --restart-from 41 &
- #############################################################
-
- pid=$! && touch step2.pid$pid.started
- wait $pid && touch step2.pid$pid.ended
-
- fi
-
- #-- check results
- myecho "without_bloocoo_restart_on_error : check results... "
- diff $ASB_REF_without_bloocoo_debug_mode_1_run1 $ASB_without_bloocoo_restart_on_error_run1 > /dev/null
- [ $? -eq 0 ] && { myecho "OK, same results"; } || { myecho "WARNING!! results differ..."; }
-}
-
-#---------------------------------------------------------------------------------------
-# 1.2 Without bloocoo, with restart TO RESUME ITERATIONS
-#---------------------------------------------------------------------------------------
-
-without_bloocoo_restart_for_more_iterations () {
- # cutoffs: [(21, 2), (41, 2), (61, 2), (81, 2)]
- [ -z $1 ] && { myecho "Missing argument"; exit; }
-
- TMPDIR=$WORKDIR/without_bloocoo_debug_mode_1_restart_for_more_iterations/run-1
- export ASB_without_bloocoo_debug_mode_1_restart_for_more_iterations_run1=$TMPDIR/assembly.fasta
-
- myecho "without_bloocoo_restart_for_more_iterations"
- if [ "$1" != "YES" ]; then # only useful to recall ABS_ env. variable
- myecho "no run"
-
- else
- [ -d $TMPDIR ] && { myecho "Cleaning $TMPDIR..."; rm -rf $TMPDIR; }
- mkdir -p $TMPDIR && cd $TMPDIR
-
- #-- step 1 : first set of iterations (21,41,61)
- myecho "without_bloocoo_restart_for_more_iterations : start iterations..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 --no-error-correction $DATA_OPTIONS --kmer-sizes 21,41,61&
- #############################################################
-
- pid=$! && touch step1.pid$pid.started
- wait $pid && touch step1.pid$pid.ended
-
- #-- step 2 : continue iterations (81)
- myecho "without_bloocoo_restart_for_more_iterations : resume iterations..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 --no-error-correction $DATA_OPTIONS --restart-from 81&
- #############################################################
-
- pid=$! && touch step2.pid$pid.started
- wait $pid && touch step2.pid$pid.ended
-
- fi
-
- #-- check results
- myecho "without_bloocoo_restart_for_more_iterations : check results..."
- diff $ASB_REF_without_bloocoo_debug_mode_1_run1 \
- $ASB_without_bloocoo_debug_mode_1_restart_for_more_iterations_run1 > /dev/null
- [ $? -eq 0 ] && { myecho "OK, same results"; } || { myecho "WARNING!! results differ..."; }
-}
-
-
-########################################################################################
-# 2. With Bloocoo (default)
-########################################################################################
-
-#---------------------------------------------------------------------------------------
-# 2.1 Runs with bloocoo (single-threaded OR multi-threaded), without restart
-#---------------------------------------------------------------------------------------
-with_bloocoo_reference () {
- [ -z $1 ] && { myecho "Missing argument"; exit; }
-
- #-- minia single-threaded + bloocoo single-threaded
- myecho "with_bloocoo_reference : reference run-1..."
- WORKDIR_subdir=with_bloocoo_debug_mode_1
- for runId in $reproductibility_iterations; do
- TMPDIR=$WORKDIR/$WORKDIR_subdir/run-$runId
- mkdir -p $TMPDIR && cd $TMPDIR
- [ "$1" = "YES" ] && { time $GATB_script --debug 1 $DATA_OPTIONS; } || { myecho "no run"; }
- eval export ASB_REF_with_bloocoo_debug_mode_1_run${runId}=$TMPDIR/assembly.fasta
- done
-
- #-- minia single-threaded + bloocoo multi-threaded
- myecho "with_bloocoo_reference : reference run-2..."
- WORKDIR_subdir=with_bloocoo_debug_mode_2
- for runId in $reproductibility_iterations; do
- TMPDIR=$WORKDIR/$WORKDIR_subdir/run-$runId
- mkdir -p $TMPDIR && cd $TMPDIR
- [ "$1" = "YES" ] && { time $GATB_script --debug 2 $DATA_OPTIONS; } || { myecho "no run"; }
- eval export ASB_REF_with_bloocoo_debug_mode_2_run${runId}=$TMPDIR/assembly.fasta
- done
-
- #-- check results (compare run-1 and run-2), should be identical
- myecho "with_bloocoo_reference : check that run-1 and run-2 have the same results..."
- myecho " run-1 : minia single-threaded + bloocoo single-threaded"
- myecho " run-2 : minia single-threaded + bloocoo multi-threaded"
- diff $ASB_REF_with_bloocoo_debug_mode_1_run1 $ASB_REF_with_bloocoo_debug_mode_2_run1 > /dev/null
- [ $? -eq 0 ] && { myecho "OK, same results"; } || { myecho "WARNING!! results differ..."; }
-}
-
-#---------------------------------------------------------------------------------------
-# 2.2 Runs with bloocoo (single-threaded case ONLY, to simplify), with restart ON ERROR
-#---------------------------------------------------------------------------------------
-with_bloocoo_restart_on_error () {
- [ -z $1 ] && { myecho "Missing argument"; exit; }
-
- myecho "with_bloocoo_restart_on_error"
- TMPDIR=$WORKDIR/with_bloocoo_debug_mode_1_restart_on_error/run-1
- export ASB_with_bloocoo_debug_mode_1_restart_on_error_run1=$TMPDIR/assembly.fasta
-
- if [ "$1" != "YES" ]; then # only useful to recall ABS_ env. variable
- myecho "no run"
-
- else
- [ -d $TMPDIR ] && { myecho "Cleaning $TMPDIR..."; rm -rf $TMPDIR; }
- mkdir -p $TMPDIR && cd $TMPDIR
-
- #-- step 1 : emulate an error
- myecho "with_bloocoo_restart_on_error : emulate an error..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 $DATA_OPTIONS &
- #############################################################
-
- pid=$! && touch step1.pid$pid.started
-
- WATCH_FILE=assembly.list_reads.41
- while [ ! -f $WATCH_FILE ]; do sleep 2; done
-
- touch step1.pid$pid.killed
- killall python memused minia
-
- myecho "with_bloocoo_restart_on_error: continue"
- sleep 5
-
- #-- step 2 : resume interrupted simulation (restart on error)
- myecho "with_bloocoo_restart_on_error : resume interrupted simulation (restart on error)..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 $DATA_OPTIONS --restart-from 41 &
- #############################################################
-
- pid=$! && touch step2.pid$pid.started
- wait $pid && touch step2.pid$pid.ended
-
- fi
-
- #-- check results
- myecho "with_bloocoo_restart_on_error : check results..."
- diff $ASB_REF_with_bloocoo_debug_mode_1_run1 \
- $ASB_with_bloocoo_debug_mode_1_restart_on_error_run1 > /dev/null
- [ $? -eq 0 ] && { myecho "OK, same results"; } || { myecho "WARNING!! results differ..."; }
-}
-
-#---------------------------------------------------------------------------------------
-# 2.3 Runs with bloocoo (single-threaded case ONLY), with restart to RESUME ITERATIONS
-#---------------------------------------------------------------------------------------
-with_bloocoo_restart_for_more_iterations () {
- # cutoffs: [(21, 2), (41, 2), (61, 2), (81, 2)]
-
- [ -z $1 ] && { myecho "Missing argument"; exit; }
-
- TMPDIR=$WORKDIR/with_bloocoo_debug_mode_1_restart_for_more_iterations/run-1
- export ASB_with_bloocoo_debug_mode_1_restart_for_more_iterations_run1=$TMPDIR/assembly.fasta
-
- myecho "with_bloocoo_restart_for_more_iterations"
- if [ "$1" != "YES" ]; then # only useful to recall ABS_ env. variable
- myecho "no run"
-
- else
- [ -d $TMPDIR ] && { myecho "Cleaning $TMPDIR..."; rm -rf $TMPDIR; }
- mkdir -p $TMPDIR && cd $TMPDIR
-
- #-- step 1 : first set of iterations (21,41,61)
- myecho "with_bloocoo_restart_for_more_iterations : start iterations..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 $DATA_OPTIONS --kmer-sizes 21,41& # not 61 because of small_test_reads.fa.gz
- #############################################################
-
- pid=$! && touch step1.pid$pid.started
- wait $pid && touch step1.pid$pid.ended
-
- #-- step 2 : continue iterations (81)
- myecho "with_bloocoo_restart_for_more_iterations : resume iterations..."
-
- ############################ RUN ############################
- $GATB_script --debug 1 $DATA_OPTIONS --restart-from 61&
- #############################################################
-
- pid=$! && touch step2.pid$pid.started
- wait $pid && touch step2.pid$pid.ended
-
- fi
-
- #-- check results
- myecho "with_bloocoo_restart_for_more_iterations : check results..."
- diff $ASB_REF_with_bloocoo_debug_mode_1_run1 \
- $ASB_with_bloocoo_debug_mode_1_restart_for_more_iterations_run1 > /dev/null
- [ $? -eq 0 ] && { myecho "OK, same results"; } || { myecho "WARNING!! results differ..."; }
-}
-
-########################################################################################
-########################################################################################
-################## ################
-################## M A I N ################
-################## ################
-########################################################################################
-########################################################################################
-
-init_env
-
-mkdir -p $WORKDIR
-cd $WORKDIR
-
-#---------------------------------------------------------------------------------------
-# I. Reference runs (no restart)
-#---------------------------------------------------------------------------------------
-
-#reproductibility_iterations="1 2 3 4 5"
-reproductibility_iterations="1"
-
-#-- without bloocoo, reference simulations (repeat runs to check reproductibility)
-without_bloocoo_reference YES # OK
-
-#-- with bloocoo, reference simulations (repeat runs to check reproductibility)
-with_bloocoo_reference YES # OK
-
-#---------------------------------------------------------------------------------------
-# II. Test restart feature
-#---------------------------------------------------------------------------------------
-
-myecho "-----------------------------"
-
-#-- without bloocoo, 2 restart scenarios
-
-without_bloocoo_restart_on_error YES # OK
-without_bloocoo_restart_for_more_iterations YES # OK
-
-#-- with bloocoo
-
-with_bloocoo_restart_on_error YES # OK
-with_bloocoo_restart_for_more_iterations YES # OK
-
-#---------------------------------------------------------------------------------------
-# Summary of assembly files to be checked
-#---------------------------------------------------------------------------------------
-
-#wc -l $WORKDIR/with*/run-*/assembly.fasta
-myecho
-myecho "md5sum of all assembly.fasta files (in the WORKDIR tree)..."
-md5sum $WORKDIR/with*/run-*/assembly.fasta
-
-myecho
-myecho "List of assembly files to compare (to check results)..."
-env | grep ASB_ | sort
-
-ASB_LIST="`env | grep ASB_ | sort | cut -d= -f1`"
-
-myecho
-for ASB_FILE in $ASB_LIST; do
- eval "test -f \$$ASB_FILE"
- [ $? -eq 0 ] && { msg="found"; } || { msg=" !!! NOT found !!!"; }
- myecho "File $ASB_FILE $msg"
-done
diff --git a/external/gatb-minia-pipeline/gatb b/external/gatb-minia-pipeline/gatb
deleted file mode 100755
index e7388df9a1d24c8abcafedcce450f066e354e570..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/gatb
+++ /dev/null
@@ -1,626 +0,0 @@
-#!/usr/bin/env python2
-
-import sys, os, shutil
-from subprocess import call, Popen, PIPE, STDOUT, check_output
-import glob
-
-if 3 > int(sys.version[0]): # only works in python 2
- sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) #unbuffered print, solves badly ordered stdout on clusters
-
-prefix="assembly"
-
-doc = """GATB Pipeline
-
-Usage:
-
- %s [arguments]
-
-Reads (mandatory, specify at least one of these parameters):
-
- --12 <filename> interleaved paired reads
- -1 <filename> non-interleaved paired reads (forward mates)
- -2 <filename> (reverse mates)
- -s <filename> single reads
- -l <file_of_filenames> list of single reads, one file name per line
- --mp-12 <filename> same input as paired reads (--12) but for mate pairs
- --mp-1 <filename> same input as paired reads (-1 -2) but for mate pairs
- --mp-2 <filename>
-
-Advanced parameters (optional):
-
- -o <string> prefix of the output files (default: assembly)
- -c <filename> filename of contigs, will only perform scaffolding+gapfilling
- --step <step> step size to control increments of k values (default: 20)
- --kmer-sizes <k1>,<k2>,.. comma-separated list of k-mer sizes (default: 21,21+step,21+2*step,..)
- --abundance-mins <t1>,<t2>,.. list of low abundance thresholds (default: 2,2,2,..)
- --max-memory <int> go faster by using more memory (in MB) (default: as much as Minia needs)
- --restart-from <k> k value where to restart the multi-k process (useful for interrupted jobs)
- --continue-scaffolding continue an interrupted scaffolding (already mapped libraries are not remapped;
- should be used along with -c <assembly_kXXX.fa>)
- --no-scaffolding skips scaffolding
- --no-error-correction skips error correction
- --besst_iter <int> number of iteration during Besst scaffolding (default:10000)
-
- --nb-cores <int> number of core to use with Bloocoo and Besst (default: all)
-
-""" % (sys.argv[0])
-
-paired_reads = []
-mate_pairs = []
-unpaired_reads = []
-contigs = None
-list_k_values = []
-list_min_abundances = []
-k_restart = -1
-step = 20
-max_memory = -1
-debug_mode = 0 # 0: no debugging
-skip_scaffolding = 0 # 0: do scaffolding
-
-nb_cores_bloocoo=None
-nb_cores_besst=None
-nb_cores_minia=None
-
-
-
-# it's a hardcoded switch; only switch to sspace if you have good reasons to dislike besst! because besst rocks.
-#scaffolding_method="sspace"
-scaffolding_method="besst"
-
-# Set them to true to enable bloocoo
-use_bloocoo_preprocessing = False# used to launch bloocoo
-bloocoo_mode = False# used in restart mode (bloocoo _not_ launched)
-
-continue_scaffolding = False
-besst_iter = 10000
-l_minia_reads = [] # list of filenames used by minia
-
-try:
- skip = 1 # this was formerly to handle paired-end case (-p XX XX) but it's not needed anymore now
- library = ""
- for i,arg in enumerate(sys.argv):
- if skip > 0:
- skip -= 1
- continue
- skip = 1
- if arg == "--12" or arg == "--mp-12":
- library = sys.argv[i+1]
- paired_reads.append(library) # list of all pairendd/matepairs reads
- if arg == "--mp-12":
- mate_pairs.append(library) # remember which are matepairs
- elif arg == "-1" or arg == "--mp-1":
- library = sys.argv[i+1]
- elif arg == "-2" or arg == "--mp-2":
- if library == "":
- exit("missing -1 parameter")
- library += " " + sys.argv[i+1]
- paired_reads.append(library) # list of all pairendd/matepairs reads
- if arg == "--mp-2":
- mate_pairs.append(library) # remember which are matepairs
- library = ""
- elif arg == "-s":
- unpaired_reads.append(sys.argv[i+1])
- elif arg == "-c":
- contigs = sys.argv[i+1]
- elif arg == "--kmer-sizes":
- list_k_values = list(map(int,sys.argv[i+1].split(',')))
- elif arg == "--abundance-mins":
- list_min_abundances = list(map(int,sys.argv[i+1].split(',')))
- elif arg == "-l":
- unpaired_reads = open(sys.argv[i+1]).read().splitlines()
- elif arg == "-o":
- prefix = sys.argv[i+1]
- elif arg == "--restart-from":
- k_restart = int(sys.argv[i+1])
- use_bloocoo_preprocessing = False #no ec when continuing, of course
- elif arg == "--step":
- step = int(sys.argv[i+1])
- elif arg == "--max-memory":
- max_memory = int(sys.argv[i+1])
- elif arg == "--nb-cores":
- nb_cores_minia = int(sys.argv[i+1])
- nb_cores_bloocoo = int(sys.argv[i+1])
- nb_cores_besst = int(sys.argv[i+1])
- elif arg == "--besst_iter":
- besst_iter = int( sys.argv[i+1] )
-
- # special cases: 0-parameters arguments, need for "skip=0", well one day i'll use getopt
- elif arg == "--sspace": #hidden parameter, for now
- scaffolding_method = "sspace"
- skip = 0
- elif arg == "--no-error-correction":
- use_bloocoo_preprocessing = False
- bloocoo_mode = False
- skip = 0
- elif arg == "--continue-scaffolding":
- continue_scaffolding = True
- skip = 0
- elif arg == "--no-scaffolding":
- skip_scaffolding = 1
- skip = 0
-
- elif arg in ["-h", "-help", "--help"]:
- raise Exception("Displaying help")
-
- # debug mode
- elif arg == "--debug":
- debug_mode = int(sys.argv[i+1])
- else:
- print("Unknown parameters", arg)
- raise Exception("Displaying help")
- if len(paired_reads) + len(unpaired_reads) == 0:
- raise Exception("Please input at least one read dataset")
-except:
- import traceback
- traceback.print_exc()
- print(doc)
- sys.exit(1)
-
-from sys import platform
-if platform == "darwin":
- exit("gatb-pipeline requires a Linux 64 bits system")
-
-
-#-- multi-threading parameters
-if( None == nb_cores_bloocoo ):
- try:
- nb_cores_system = int(check_output(["nproc"]))
- except ValueError:
- print("machine has no nproc, setting threads to 1")
- nb_cores_system = 1
-
- nb_cores_bloocoo = nb_cores_system # for bloocoo
- nb_cores_besst = nb_cores_system # for besst
-
-#-- debug mode
-if debug_mode == 0 :
- print("No debugging option")
-elif debug_mode == 1 :
- nb_cores_bloocoo = 1
- print("debug_mode=%d : minia single-threaded, bloocoo [if used] single-threaded" % debug_mode)
-elif debug_mode == 2 :
- print("debug_mode=%d : minia single-threaded, bloocoo [if used] multi-threaded (with nb_cores_bloocoo=%d)" % (debug_mode, nb_cores_bloocoo))
-else :
- print("Error in --debug option")
- sys.exit(1)
-
-
-DIR = os.path.dirname(os.path.realpath(__file__))
-
-from time import gmtime, strftime
-class Logger(object):
- def __init__(self):
- global prefix
- with open(prefix + ".log","w") as logfile:
- self("GATB-pipeline starting")
- self("Command line: %s \n\n" % ' '.join(sys.argv))
- def __call__(self, message):
- global prefix
- message = ("(%s) " % strftime("%Y-%m-%d %H:%M:%S", gmtime()))+ message
- logfile= open(prefix + ".log", "a")
- sys.stderr.flush()
- sys.stdout.write(message+"\n")
- sys.stdout.flush()
- logfile.write(message+"\n")
- logfile.flush()
- logfile.close()
-log = Logger()
-
-def execute(program, cmdline=[], interpreter=None, stdout=None, memused=False):
- ret = 0
- try:
- cmd = []
- if memused:
- cmd += [ "%s/tools/memused" % DIR ]
- if interpreter:
- cmd += [interpreter]
- if program is not None:
- cmd += [ "%s/%s" % (DIR, program) ]
- cmd += map(str, cmdline)
- program_string = ((interpreter + " ") if interpreter is not None else "") + (program if program is not None else "")
- log("Execution of '%s'. Command line: \n %s" % (program_string, ' '.join(cmd)))
- stderr = None
- log_output = stdout is None # log to file
- log_output = False # disabled logging of execute() programs, because it causes stdout/stderr to be slightly not in order (try it, you will see)
- if log_output:
- stdout=PIPE
- #stderr=STDOUT # i changed my mind, let's not capture stderr, minia outputs annoying progress bars
- p = Popen(cmd, stdout=stdout, stderr=stderr, bufsize=0) #unbuffered
- if log_output:
- global prefix
- tee = Popen(['tee', '--append', prefix + ".log"], stdin=p.stdout)
- p.stdout.close()
- tee.communicate()
- ret = p.wait()
- except OSError as e:
- log("Exception:" + str(e) )
- ret = 1
- if ret:
- log("Execution of '%s' failed. Command line: \n %s" % (program_string, ' '.join(cmd)))
- exit(1)
-
-list_reads = prefix + ".list_reads"
-final_assembly = prefix + ".fasta"
-
-
-# check that -s isnt mixed up with -l
-for ur in unpaired_reads:
- try:
- try: # some code duplication with below
- import gzip
- fp = gzip.open(ur)
- fp.read(2) # read arbitrary bytes to check if gzipped
- fp.close() # close and reopen if successful
- fp = gzip.open(ur)
- except Exception as e:
- fp.close()
- fp = open(ur)
- from tools.readfq import readfq
- for name, seq, qual in readfq(fp):
- break
- fp.close()
- except:
- import traceback
- traceback.print_exc()
-
- exit("are you sure you didn't confuse -s with -l?")
-
-
-def create_list_reads( l_reads ):
- '''create of flat text file with l_reads'''
- with open( list_reads, 'w' ) as f:
- for read in l_reads:
- for filename in read.strip().split():
- if not os.path.exists(filename):
- exit("Read file %s does not exist" % filename)
- f.write( filename + "\n" )
-
-def sav_list_reads( suffix ):
- if( os.path.exists( list_reads ) ):
- shutil.copyfile( list_reads, ".".join( [list_reads, suffix] ) )
-
-# ------------------------------
-# minia
-
-def minia(k, min_abundance, prefix):
- global contigs
- if k == 0:
- exit('cannot execute minia with k=0')
-
- params = ['-in', list_reads, '-kmer-size', k, '-abundance-min', min_abundance, '-out', prefix]
-
- if max_memory != -1:
- params += ['-max-memory',max_memory]
-
- if k >= 128:
- params += ['-debloom','original'] # fix for large k values
-
- if nb_cores_minia is not None:
- params += ['-nb-cores',nb_cores_minia]
-
- if ( 1 <= debug_mode <= 2) :
- params += ['-nb-cores','1'] # issue54
-
- execute('minia/minia', params, memused=True)
- contigs = prefix + ".contigs.fa"
- return contigs
-
-# ------------------------------
-# wrapper for bloocoo
-
-def bloocoo(output_file_prefix, threshold=2, kmer_size=31):
-
- # bloocoo command line arguments
- keyword = ".corrected_with_bloocoo"
- corrected_fasta = output_file_prefix + keyword + ".fa"
- params = ['-file', list_reads, '-out', corrected_fasta, '-abundance-min', threshold,
- '-kmer-size', kmer_size, '-nb-cores', nb_cores_bloocoo , '-slow', '-high-precision']
- log("Running bloocoo on %d cores" % nb_cores_bloocoo)
-
- # call bloocoo
- execute('bloocoo/Bloocoo', params)
- log("Bloocoo done\n\n")
-
- return bloocoo_list_corrected(output_file_prefix, list_reads, corrected_fasta, keyword)
-
-#-------------------------------
-# bloocoo helper
-
-def bloocoo_list_corrected(c_output_file_prefix, c_list_reads, c_corrected_fasta, c_keyword):
-
- log("Calling bloocoo_list_corrected...")
-
- # 2 cases: one or several input banks (cf. Bloocoo.cpp)
- # according to the number of lines of the list_reads file
- with open(c_list_reads) as f:
- nInputBanks = sum(1 for _ in f) # nb of lines in list_reads
-
- log("Bloocoo used %d input file(s)\n\n" % nInputBanks)
-
- if nInputBanks == 1: # one input bank
- return [ c_corrected_fasta ]
- elif nInputBanks > 1: # several input banks
- c_list_corrected = sorted(glob.glob(c_output_file_prefix+'*'+c_keyword+'*_*_*'))
- if len(c_list_corrected) != nInputBanks:
- print("Error: Bloocoo returned fewer error-corrected files (%d) than original input files (%d)" % (len(bloocoo_output), nInputBanks))
- exit(1)
- return c_list_corrected
- else:
- log("Error: nInputBanks=%d " % nInputBanks)
-
-
-
-
-
-def get_paired_end_parameters(contigs, library, is_mate_pairs = False):
- paired_reads = library.split(' ')
- cmd = ["%s/tools/estimate-insert-sizes" % DIR, contigs] + paired_reads
- if is_mate_pairs:
- cmd += ["--RF"] # force mate pairs
- output = Popen(cmd, stdout=PIPE).communicate()[0]
- orientation, mean, stdev = None, None, None
- for line in output.split('\n'):
- if line.startswith('Orientation'):
- l = line.split()
- orientation, mean, stdev = l[1], int(l[3]), int(l[5])
- log("GATB-Pipeline estimated insert size of library " + str(paired_reads) + " : %f %f %s " %(mean, stdev, orientation ))
- return orientation, mean, stdev
-
-def possibly_gunzip(filename, lib_index, paired_index=None):
- if filename.endswith('.gz'):
- unzipped_filename = '.'.join(filename.split(".")[:-1])
- ext = unzipped_filename.split(".")[-1]
- output = prefix + '.lib%d' % lib_index
- if paired_index:
- output += "_%d" % paired_index
- output += "." + ext
- log("Gunzipping " + str(filename) + " to " + str(output))
- outfile = open(output, 'wb')
- execute(None, ['-c', filename], interpreter='gunzip', stdout=outfile)
- outfile.close
- return output
- return filename
-
-def sspace(contigs, paired_reads, output_filename=""):
- # create a sspace config file
- lib_file = prefix + '.sspace.config'
- with open(lib_file, 'w') as f:
- for i, library in enumerate(paired_reads):
- is_mate_pairs = library in mate_pairs
- # sspace needs de-interleaved input
- if ' ' not in library:
- library = possibly_gunzip(library, i)
- log("Splitting interleaved file: " +str(library))
- ext = library.split(".")[-1]
- p1, p2 = [prefix + ".lib%d_%d." % (i,j) + ext for j in [1,2] ]
- #de-interleave reads using SGA's script (was too lazy to write my own)
- execute('tools/sga-deinterleave.pl', [library, p1, p2], interpreter="perl")
- library = p1 + " " + p2
- else:
- # sspace basic cannot work with gzipped files
- p1, p2 = library.split(' ')
- library = possibly_gunzip(p1, i, 1) + ' ' + possibly_gunzip(p2, i, 2)
-
- # estimate insert size
- orientation, mean, stdev = get_paired_end_parameters(contigs, library, is_mate_pairs)
- if orientation is None:
- exit("Error running estimate-insert-sizes for library: %s" % library)
-
- # sspace error isn't exactly the stdev; subjectively, I'm converting using 3 sigmas
- error = min(max(0.1, stdev * 3.0 / mean),0.9)
- f.write('lib%d %s %d %0.1f %s\n' % (i, library, mean, error, orientation))
-
- # run sspace
- cmd = ['-l', lib_file, '-s', contigs, '-b', prefix + '.sspace']
- execute('sspace/SSPACE_Basic_v2.0.pl', cmd, interpreter="perl", memused=True)
- log("SSPACE is done! the maximal memory used above was for SSPACE only")
-
- # clean up intermediate sspace files
-
-
-# ------------------------------
-# besst wrapper
-
-# besst and its script needs python >= 2.7 < 3, see if we have it installed on the system somewhere
-def check_for_python_27():
- for i, python27 in enumerate(['python', 'python2', 'python2.7', 'python-2.7']):
- try:
- ret = call([python27, "-c", "from collections import Counter"],stdout=PIPE,stderr=PIPE)
- #also need to make sure it's not python3 (BESST doesn't support it)
- ret = call([python27, "-c", "import sys; assert(int(sys.version[0]) == 2)"],stdout=PIPE,stderr=PIPE)
- except:
- ret = 1
- if ret == 0:
- if i > 0:
- log("found Python 2.7 via command: " + str(python27))
- return python27
- exit("BESST needs Python >= 2.7 and < 3, make sure it is aliased to either the 'python' or the 'python2.7' command on your shell")
-
-
-def run_besst_mapping(i, contigs, library):
- interpreter = check_for_python_27()
- # besst needs de-interleaved input, for the mapping phase (else it thinks they're single end)
- if ' ' not in library:
- library = possibly_gunzip(library, i) # until sga-deinterleave supports gzipped input, no other choice but to gunzip
- log("Splitting interleaved file: " + str(library))
- ext = library.split(".")[-1]
- p1, p2 = [prefix + ".lib%d_%d." % (i,j) + ext for j in [1,2] ]
- #de-interleave reads using SGA's script (was too lazy to write my own)
- execute('tools/sga-deinterleave.pl', [library, p1, p2], interpreter="perl")
- library = p1 + " " + p2
- paired_reads = library.split(' ')
-
- output_bam = prefix + '.lib_%d' % i
- os.environ["TEMP"] = os.getcwd() # besst uses tempfile which uses $TEMP to store mapping data
- done_file = output_bam + ".bam.done"
- if os.path.exists(done_file) and continue_scaffolding:
- log("Reusing existing BAM file for library " + str(library))
- else:
- execute('BESST/scripts/reads_to_ctg_map.py', ["--tmp_path", os.path.dirname(os.path.realpath(output_bam)) + os.sep + "BESST_tmp"] + ["--threads", nb_cores_besst] + paired_reads + [contigs, output_bam], interpreter=interpreter)
- open(done_file, 'a').close()
- return output_bam + ".bam"
-
-def besst(contigs, bam_files, orientations, output_filename="" ):
- global k, final_assembly, besst_iter
- interpreter = check_for_python_27()
- #filter_contigs = (200 if len(mate_pairs) == 0 else 1000) #hacky
- #cmd = ['-c', contigs, '-f'] + bam_files + ['--orientation'] + orientations + ['-filter_contigs', filter_contigs, '-o', prefix + '_besst', '-K', k]
- # let's try with as few parameters as possible
- cmd = ['-c', contigs, '-f'] + bam_files + ['-o', prefix + '_besst'] + ['-orientation'] + orientations + ['--iter', besst_iter]
- execute('BESST/runBESST', cmd, interpreter=interpreter, memused=True)
- besst_scaffolds = sorted(glob.glob(prefix + "_besst/BESST_output/pass*/*.fa"))
- if len(besst_scaffolds) == 0:
- exit("Error: BESST returned no results in %s" % (prefix + "_besst/"))
- last_pass = besst_scaffolds[-1]
- if os.path.exists(final_assembly):
- os.remove(final_assembly)
- os.symlink(last_pass, final_assembly)
- log( "BESST is done! the maximal memory used above was for BESST only")
-
-
-# ------------------------------
-# wrapper for scaffolding
-
-def scaffold(contigs, paired_reads):
- if scaffolding_method == "sspace":
- sspace(contigs,paired_reads)
- elif scaffolding_method == "besst":
- # besst needs pre-mapping one library at a time
- bam_files, orientations = [], []
- for i, paired_read in enumerate(paired_reads):
- bam_files += [run_besst_mapping(i,contigs,paired_read)]
- orientations += [ 'rf' if paired_read in mate_pairs else 'fr' ]
- besst(contigs,bam_files, orientations )
-
-# ------------------------------
-# auxiliary function
-
-def get_read_length(list_reads):
- read_lengths = []
- for library in list_reads:
- if ' ' in library:
- reads_list = library.split(' ')
- else:
- reads_list = [library]
- for reads_file in reads_list:
- try:
- import gzip
- fp = gzip.open(reads_file)
- fp.read(2) # read arbitrary bytes to check if gzipped
- fp.close() # close and reopen if successful
- fp = gzip.open(reads_file)
- except Exception as e:
- fp.close()
- fp = open(reads_file)
- # read the 1000 first reads
- from tools.readfq import readfq
- read_count = 0
- for name, seq, qual in readfq(fp):
- read_count += 1
- read_lengths += [len(seq)]
- if read_count > 1000:
- break
- fp.close()
-
- # so, on CEA cluster, loading numpy forced minia to run on a single thread. so let's not use numpy here. days of debugging to get that.
- import math
- def percentile(data, percentile):
- size = len(data)
- return sorted(data)[int(math.ceil((size * percentile) / 100)) - 1]
-
- if len(read_lengths) == 0:
- print("WARNING: couldn't detect max read length. Are you sure the input is correct?")
- exit(1)
-
- estimated_max_read_length = percentile(read_lengths,90)
- log("Setting maximum kmer length to: " + str(estimated_max_read_length) + " bp") # based on the 90 percentile of 1000 first reads lengths of each input file
- return estimated_max_read_length
-
-# ------------------------------
-# main pipeline
-
-if contigs is None: # need to create contigs, or are they given?
- create_list_reads( paired_reads + unpaired_reads )
-
- if use_bloocoo_preprocessing == True:
-
- # call bloocoo
- l_reads_corrected = bloocoo(output_file_prefix=prefix)
-
- # now list_reads contains only the bloocoo output filename(s)
- sav_list_reads( "orig" )
-
- # I copy into unpaired_reads because paired_reads are used in scaffolding, not unpaired.
- l_minia_reads = l_reads_corrected
- else:
- if ( k_restart != -1 and bloocoo_mode == True ): # whenever we have both --restart-from and bloocoo
- keyword = ".corrected_with_bloocoo"
- corrected_fasta = prefix + keyword + ".fa"
- l_minia_reads = bloocoo_list_corrected(prefix, list_reads, corrected_fasta, keyword)
- else:
- l_minia_reads = paired_reads + unpaired_reads
-
-
-
- # minia preparation
- if len(list_k_values) == 0:
- max_k = get_read_length( l_minia_reads ) #TODO: modify bloocoo so that it gives a read length histogram, rather than using this hacky procedure to get max read length
- if max_k <= 21:
- sys.exit("Reads are shorter than 21 base pairs? (%d bp at 90 percentile of read lengths over the first 1000 reads of each input file).\nNotify a developer if this estimation was wrong, or if your reads are really that short, please set the list of kmer lengths manually using the --kmer-sizes parameter" % max_k)
- # two implicit assumptions: do not make more than 20 rounds, and start at k=21
- for i in range(20):
- k = 21 + i*step
- if k <= max_k and k <= 256: #max supported in minia binary is 256
- list_k_values += [k]
-
- if len(list_min_abundances) == 0:
- list_min_abundances = [2]*len(list_k_values)
-
- if len(list_min_abundances) == 1 and len(list_k_values) > 1:
- list_min_abundances = [list_min_abundances[0]]*len(list_k_values)
-
- cutoffs = sorted(zip(list_k_values, list_min_abundances))
-
- if k_restart == -1:
- log("Multi-k values and cutoffs: " + str(cutoffs) + "\n\n")
- else:
- log("*** restart mode")
- cutoffs_keys = sorted([x for x in dict(cutoffs).keys()])
- last_k_value_before_restart = cutoffs_keys[cutoffs_keys.index(k_restart)-1]
- log("*** pipeline restart mode: k_restart=%d (last_k_value_before_restart=%d) *** " % (k_restart, last_k_value_before_restart))
- cutoffs = sorted([(key,dict(cutoffs)[key]) for key in cutoffs_keys if key >= k_restart])
- log("Restarting GATB-pipeline with cutoffs " + str(cutoffs))
- log("This assumes that an assembly with k =" + str(last_k_value_before_restart) + " exists.")
-
- last_k_value = 0
- previous_contigs = None if k_restart == -1 else prefix+"_k%d.contigs.fa"%last_k_value_before_restart
- """
- multi-k minia iteration happens here
- """
- for k in sorted(dict(cutoffs).keys()):
- min_abundance = dict(cutoffs)[k]
- log("Minia assembling at k=%d min_abundance=%d" % (k, min_abundance))
- extra_reads = [previous_contigs]*(min_abundance+1) if previous_contigs is not None else []
- create_list_reads( l_minia_reads + extra_reads )
- sav_list_reads( str(k) ) # create a copy for dbg purpose
- multi_k_prefix = prefix + "_k%d" % k
- previous_contigs = minia(k, min_abundance, prefix=multi_k_prefix)
- last_k_value = k
- log("Finished Minia k=%d\n\n" % last_k_value)
- k = last_k_value # hint for besst
- os.symlink(previous_contigs.rsplit("/", 1)[-1], prefix+"_final.contigs.fa") # create system link in same location as files
- log("Finished Multi-k GATB-Pipeline at k=%d\n\n" % last_k_value)
-
-# scaffolding all libraries
-if (skip_scaffolding == 0):
- if len(paired_reads) > 0:
- scaffold(contigs, paired_reads)
- else:
- if os.path.exists(final_assembly):
- os.remove(final_assembly)
- os.symlink(contigs, final_assembly)
- log("Finished scaffolding. Scaffolds are in: %s" % final_assembly)
-else:
- log("Skipped scaffolding.")
-
-log("Pipeline finished!")
diff --git a/external/gatb-minia-pipeline/minia/minia b/external/gatb-minia-pipeline/minia/minia
deleted file mode 100755
index 84944ec11c1c904f8c58de1c9e789835e0cf6eb2..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/minia/minia and /dev/null differ
diff --git a/external/gatb-minia-pipeline/release.sh b/external/gatb-minia-pipeline/release.sh
deleted file mode 100755
index 13fe6f739710e91bebd1f59c72b4aa3af617abc1..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/release.sh
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/bin/bash
-
-soft=gatb-pipeline
-
-if [[ "$1" == "--version" ]] # version override
-then
- version=$2
- version_override="--override"
-else
- #make a version number
- version="1.`git rev-list HEAD | wc -l`"
-fi
-echo "version: $version"
-
-rm -Rf $soft-$version/
-mkdir $soft-$version
-
-# create a changelog
-git log --pretty=format:'%cd: %s' --date=short > CHANGELOG
-echo "" >> CHANGELOG # it was missing a \n
-
-# minia binary is provided for now
-cp -R minia $soft-$version/
-# extract minia release to minia/
-#tar xf dependencies/minia* -C $soft-$version/
-#mv $soft-$version/minia*/ $soft-$version/minia
-
-# package the rest
-cp gatb README.md CHANGELOG Makefile $soft-$version/
-mv $soft-$version/README.md $soft-$version/README
-mkdir -p $soft-$version/test/
-cp -R test/small_test_reads.fa.gz $soft-$version/test/
-cp -R BESST $soft-$version/
-cp -R tools $soft-$version/
-cp -R bloocoo $soft-$version/
-
-tar -chzf $soft-$version.tar.gz $soft-$version/
-rm -Rf $soft-$version/
-
-if [ "$1" == "--just-pack" ]
-then
- exit 0
-fi
-
-# uploading to gatb website
-
-#ripped from Delivery.cmake, I know, sorry for duplicating code; this needs to
-# be converted to cmake someday
-
-CPACK_DATE=$(date +"%m-%d-%Y")
-CPACK_SYSTEM_NAME=Linux
-CPACK_SYSTEM_NAME_SRC=all
-
-CMAKE_PROJECT_NAME="gatb-pipeline"
-PROJECT_NAME="gatb-pipeline"
-CPACK_PACKAGE_NAME="gatb-pipeline"
-CPACK_VERSIONS_FILENAME="versions.txt"
-
-CPACK_PACKAGE_VERSION=$version
-CPACK_USER_NAME=chikhi
-CPACK_SERVER_ADDRESS="${CPACK_USER_NAME}@scm.gforge.inria.fr"
-CPACK_SERVER_DIR="/home/groups/${PROJECT_NAME}/htdocs/versions/"
-CPACK_SERVER_VERSIONS="${CPACK_SERVER_DIR}/${CPACK_VERSIONS_FILENAME}"
-CPACK_SERVER_DIR_BIN="${CPACK_SERVER_DIR}/bin/"
-CPACK_SERVER_DIR_SRC="${CPACK_SERVER_DIR}/src/"
-
-CPACK_URI_BIN="$soft-$version.tar.gz"
-CPACK_URI_SRC="$soft-$version.tar.gz"
-
-# We define the location where the bin and src targets have to be uploaded
-CPACK_UPLOAD_URI_BIN="${CPACK_SERVER_ADDRESS}:${CPACK_SERVER_DIR_BIN}"
-CPACK_UPLOAD_URI_SRC="${CPACK_SERVER_ADDRESS}:${CPACK_SERVER_DIR_SRC}"
-CPACK_UPLOAD_VERSIONS="${CPACK_SERVER_ADDRESS}:${CPACK_SERVER_VERSIONS}"
-
-# We set the text holding all the information about the delivery.
-CPACK_INFO_BIN="${CMAKE_PROJECT_NAME} bin ${PROJECT_NAME} ${CPACK_PACKAGE_VERSION} ${CPACK_DATE} ${CPACK_SYSTEM_NAME} ${CPACK_USER_NAME} ${CPACK_URI_BIN}"
-CPACK_INFO_SRC="${CMAKE_PROJECT_NAME} src ${PROJECT_NAME} ${CPACK_PACKAGE_VERSION} ${CPACK_DATE} ${CPACK_SYSTEM_NAME_SRC} ${CPACK_USER_NAME} ${CPACK_URI_SRC}"
-
-# We get the versions.txt file from the server
-echo "calling delivery.sh"
-dependencies/delivery.sh "BIN_OTHER" ${PROJECT_NAME} ${CPACK_PACKAGE_VERSION} ${CPACK_UPLOAD_VERSIONS} ${CPACK_VERSIONS_FILENAME} "${CPACK_INFO_BIN}" ${CPACK_URI_BIN} ${CPACK_UPLOAD_URI_BIN} $version_override
-dependencies/delivery.sh "SRC_OTHER" ${PROJECT_NAME} ${CPACK_PACKAGE_VERSION} ${CPACK_UPLOAD_VERSIONS} ${CPACK_VERSIONS_FILENAME} "${CPACK_INFO_SRC}" ${CPACK_URI_SRC} ${CPACK_UPLOAD_URI_SRC} $version_override
-
-# some cleanup
-rm -f versions.txt
-mv $soft-$version.tar.gz archive/
diff --git a/external/gatb-minia-pipeline/sspace/F132-01 SSPACE_Basic_User_Manual_v2.0.pdf b/external/gatb-minia-pipeline/sspace/F132-01 SSPACE_Basic_User_Manual_v2.0.pdf
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diff --git a/external/gatb-minia-pipeline/sspace/F132-02 SSPACE_Basic_Tutorial_v2.0.pdf b/external/gatb-minia-pipeline/sspace/F132-02 SSPACE_Basic_Tutorial_v2.0.pdf
deleted file mode 100755
index aa3d20465572e674a46048370f082a59571cd0f8..0000000000000000000000000000000000000000
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diff --git a/external/gatb-minia-pipeline/sspace/README b/external/gatb-minia-pipeline/sspace/README
deleted file mode 100755
index 12f6bc214e988e9b3fa13dd44090ba3dd2c1ed12..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/README
+++ /dev/null
@@ -1,485 +0,0 @@
-Scaffolding Pre-Assemblies After Contig Extension (SSPACE)
-
-SSPACE Premium v1.0 Marten Boetzer - Walter Pirovano, Aug 2011
-email: walter.pirovano@baseclear.nl
-
-
-Description
------------
-
-SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.
-
-Implementation and requirements
--------------------------------
-
-SSPACE is implemented in perl and runs on linux, MAC and windows. SSPACE is built based on SSAKE. Code of SSAKE is changed to be able to extend and scaffold pre-assembled contigs for multiple paired reads libraries.
-
-PLEASE READ:
-SSPACE tracks in memory all contigs. That means that the memory usage will increase drastically with the size of your contig data set. In addition, during contig extension single reads are extracted and mapped to the contigs. Unmapped reads are stored in memory. Again, the more reads that can not map, the bigger the dataset and the more memory is used. Just be aware of these limitations and don't be surprised if you observe a lot of data swapping to disk if you attempt to run SSPACE on a machine with little RAM.
-
-Contig extension might not be suited to work with 454-type read pair libraries. Simply because recurring base insertions/deletions errors, such as those commonly seen in homopolymeric regions, will not cluster well in the context of the SSAKE contig extension algorithm scheme. In addition, long 454 reads are less likely to map against the contigs, thus less read pairs are found and scaffolding is based on less read pairs. One possibility is to allow gaps during mapping using the ‘-g’ parameter.
-
-Citing SSPACE
-------------
-
-Thank you for using, developing and promoting this free software.
-If you use SSPACE for you research, please cite:
-
-Boetzer M, Henkel CV, Jansen HJ, Butler D and Pirovano W. 2010. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 27(4):578-579
-
-Running SSPACE
--------------
-
-e.g. perl SSPACE_Premium_v1.0.pl -l libraries.txt -s contigs.fasta -x 0 -m 32 -o 20 -t 0 -k 5 -a 0.70 -n 15 -p 0 -v 0 -z 0 -g 0 -T 1 -b standard_out
-
-Usage: ./SSPACE_Premium_v1.0.pl
-
-Required parameters:
- -l Library file containing two paired read files with insert size, error and orientation (see Manual for more information). Also possible to insert .tab files with pairing information.
- -s Fasta file containing contig sequences used for extension. Inserted paired reads are mapped to extended and non-extended contigs
-
-Extension parameters;
- -m Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 32)
- -o Minimum number of reads needed to call a base during an extension (default -o 20)
- -t Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)
- -u Single fasta/fastq file containing unpaired sequence reads
- -r Minimum base ratio used to accept a overhang consensus base (default -r 0.9)
-
-Parameters below only considered for scaffolding and are all optional;
- -k Minimum number of links (read pairs) to compute scaffold (default -k 5)
- -a Maximum link ratio between two best contig pairs. higher values lead to least accurate scaffolding. (default -a 0.70)
- -n Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -n 15)
- -z Minimum contig size used for scaffold. Filters out contigs below this size. (default –z 0, no filtering)
-
-Bowtie parameters;
- -g Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the -v option in Bowtie (default –g 0).
- -T Specifes the number of threads in Bowtie. Corresponds to the –p option in Bowtie (default –T 1).
-
-Additional options;
- -x Indicate whether to extend the contigs of -s using paired reads in -l. (-x 1=extension, -x 0=no extension, default -x 0)
- -v Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0)
- -b Base name for your output files (default -b standard_output)
- -p Make .dot file for visualisation (-p 1=yes, -p 0=no, default -p 0)
-
-
-How it works
-------------
-
-The program consists of several steps, a short overview;
-
-The first steps are reading the data and filter them. The protocol is slightly different when -x is set to either 0 or 1. We treat them separately here;
-
-With -x 0 the steps are;
-1) Read -l library file;
- A) For each library in the -l library file. Store the reads in appropriate format. Paired reads are stored in a new file with a similar read name for easy tracking of the paired read. Format is;
-
->read1.1
-AGCTGATAGATGAT
->read1.2
-GATGATAGATAGAC
-
-2) Convert the inserted contig file to appropriate format.
-
-With -x 1 the steps are;
-
-1) Read -l library file;
- A) For each library in the -l library file. Store the reads in appropriate format, similar as step 1A.
- B) For all libraries
- - store the single reads to a new file. Only reads containing only ACGT characters are stored.
-2) Extend the pre-assembled contigs
- A) Map single reads of step 1B to (-s) contig file with Bowtie.
- B) Read unmapped reads into memory.
- C) Go through each contig in the (-s) contig file, and try to extend the contig. The new contigs are stored in a new file.
-
-
-After producing either a formatted or an extended contig file, the next step is to go through each library in the -l library file and map the filtered paired reads of step 1A to the new contigs;
-
-3) Use Bowtie to map single reads of 1A to either the formatted or extended contigs. Map only reads that are on the edges of the contigs. Only reads that map to only one contig are stored in a file. Position and orientation of each read is stored in the file.
-4) Retrieve the position of each found read.
-5) Pair contigs if both reads if a paired-read are found, store the pairing information into memory. In addition, store the sequence of the pair into memory. If the sequence of a pair is already used for pairing contigs, it is not used again.
-6) Pair contigs based on the number of links (-k) and link ratio (-a)
-7) Merge, orient and order the contigs to produce scaffolds.
-
-8) If multiple libraries are in -l file, the produced scaffolds in fasta format are the input for the new library. Steps 3 till 8 are repeated for each library.
-
-A more detailed view of the six main steps are given below.
-
-Detailed view
-------------
-
-
-1. Reading libraries
-Both fasta/fastq files inserted at the -l library file are read, converted and stored in a new file. This new file is used for mapping with Bowtie (step 4), where the new naming of the headers makes it easy to backtrack the original read pair.
-
->read1.1 (read from file 1)
-ACGATGCTAT
-
->read1.2 (read from file 2)
-ACCGCGCCCC
-
-If -x 1 is set, for contig extension, single reads containing only ACGT characters are stored in a new file. The single reads are mapped to contigs at the next step.
-
-2. Mapping when -x 1
-To extend contigs, only reads that are not already present on the contigs should be used. Otherwise, reads are re-used and cause erroneous contigs, but causes also reads mapped to multiple locations/contigs (step 4). To filter these reads out, Bowtie is used. Bowtie maps the produced single reads at step 1 to the (-s) pre-assembled contigs. A file is generated with reads that did not map to the contigs. The unmapped read file is read in memory, populating a hash table keyed by unique sequence reads with pairing values representing the number of sequence occurrences. The hash is used for contig extension at the next section.
-
-3. Extending when -x 1
-Contigs are extended, when -x set to 1, using the unmapped reads with a method developed by SSAKE. With SSAKE, contigs extension is initiated by generating the longest 3'-most word (k-mer) from the unassembled read u that is shorter than the sequence read length l. Every possible 3' most k-mers will be generated from u and used in turn for the search until the word length is smaller than a user-defined minimum, m. Meanwhile, all perfectly overlapping reads will be collected in an array and further considered for 3' extension once the k-mer search is done. At the same time, a hash table c will store every base along with a coverage count for every position of the overhang (or stretches of bases hanging off the seed sequence u).
-
-Once the search complete, a consensus sequence is derived from the hash table c, taking the most represented base at each position of the overhang. To be considered for the consensus, each base has to be covered by user-defined -o (set to 20 by default). If there's a tie (two bases at a specific position have the same coverage count), the prominent base is below a user-defined ratio r, the coverage -o is to low or the end of the overhang is reached, the consensus extension terminates and the consensus overhang joined to the contig. All reads overlapping are searched against the newly formed sequence and, if found, are removed from the hash table and prefix tree. If they are not part of the consensus, they will be used to extend other contigs, if applicable. If no overlapping reads match the newly formed contig, the extension is terminated from that end and SSAKE resumes with a new contig. That prevents infinite looping through low complexity DNA sequences. In the former case, the extension resumes using the new [l-m] space to search for joining k-mers.
-
-The process of progressively cycling through 3'-most k-mer is repeated after every contig extension until nothing else can be done on that side. Since only left-most searches are possible with a prefix tree, when all possibilities have been exhausted for the 3' extension, the complementary strand of the contiguous sequence generated is used to extend the contig on the 5' end. The DNA prefix tree is used to limit the search space by segregating sequence reads and their reverse-complemented counterparts by their first eleven 5' end bases.
-
-There are three ways to control the stringency in SSPACE:
-1) Disallow contig extension if the coverage is too low (-o). Higher -o values lead to shorter contigs, but minimizes sequence misassemblies.
-2) Adjust the minimum overlap -m allowed between the contig and short sequence reads. Higher m values lead to more accurate contigs at the cost of decreased contiguity.
-3) Set the minimum base ratio -r to higher values
-
-After the sequence assembly, a file is generated with .extendedcontigs.fasta extension in the 'intermediate_results' folder. This file contains both extended and non-extended contigs.
-
-The next steps are looped through each library, present in the (-l) library file.
-
-4. Mapping unique paired reads
-
-At step 1, pairs of each library were filtered. Reads containing N's are unable to correctly map to the contigs, therefore they are not used by Bowtie. Bowtie maps the single reads to the contigs, produced either after extending (if -x 1), or after formatting (if -x 0), or after step 5 if multiple libraries are inserted on -l.
-
-Before mapping, contigs are shortened, reducing the search space for Bowtie. Only edges of the contigs are considered for mapping. Cutting of edges is determined by taking the maximal allowed distance inserted by the user in the library file (insert size and insert standard deviation). The maximal distance is insert_size + (insert_size * insert_stdev). For example, with a insert size of 500 and a deviation of 0.5, the maximal distance is 750. First 750 bases and last 750 bases are subtracted from the contig sequence, in this case.
-
-------------------------------------------
- | |
------------- ------------
- 750bp 750bp
-
-This step reduces the search space by merging the two sequences, divided by a ‘N’ character.
-
-The algorithm of mapping goes through each pair and checks its occurrence on the edges of the contigs. If both reads are found, the reads of the pair is stored and contigs could be paired in the next step. Otherwise, it is not stored and the read pair is not used for contig pairing. If a pair is previously found and used for contig pairing, the pair is not considered again. Otherwise same links between contigs are found based on same read pair, which can generate misleading results.
-
-If either of the two reads of a read pair occur on multiple contigs, one can not tell which contig should be paired. For example, the left read occurs at contigs 1 and 3, and the right read at contig 2. For this situation it is impossible to tell if contigs 1 and 2 should be paired, or contigs 1 and 3. Therefore, reads that occur multiple times on contigs are not considered for contig pairing.
-
-5a. Building scaffolds
-The final step is scaffolding. SSPACE uses an updated version of the SSAKE scaffolder for this. For each read pairs, putative contig pairs (pre-scaffolding stage) are tallied based on the position/location of the paired reads on different contigs. Contig pairs are only considered if the calculated distance between them satisfy the mean distance specified (fourth column in -l file) while allowing for a deviation (fifth column in -l file), also defined by the user. Only contig pairs having a valid gap or overlap are allowed to proceed to the scaffolding stage.
-Please note that this stage accepts redundancy of contig pairs (i.e. a given contig may link to multiple contigs, and the number of links (spanning pairs) between any given contig pair is recorded, along with a mean putative gap or overlap(-)).
-
-Once pairing between contigs is complete, the scaffolds are built using contigs as seeds. Every contig is used in turn until all have been incorporated into a scaffold.
-
-Consider the following contig pairs (AB, AC and rAD):
-
- A B
-========= ========
- -> <-
- -> <-
- -> <-
- -> <-
-
- A C
-========= ======
- -> <-
- -> <-
-
- rA D equivalent to rDA, in this order
-========= =======
- -> <-
- -> <-
- -> <-
-
-Two parameters control scaffolding (-k and -a). The -k option specifies the minimum number of links (read pairs) a valid contig pair MUST have to be considered. The -a option specifies the maximum ratio between the best two contig pairs for a given contig being extended. For example, contig A shares 4 links with B and 2 links with C, in this orientation. contig rA (reverse) also shares 3 links with D. When it's time to extend contig A (with the options -k and -a set to 2 and 0.7, respectively), both contig pairs AB and AC are considered. Since C (second-best) has 2 links and B (best) has 4 (2/4) = 0.5 below the maximum ratio of 0.7, A will be linked with B in the scaffold and C will be kept for another extension. If AC had 3 links the resulting ratio (0.75), above the user-defined maximum 0.7 would have caused the extension to terminate at A, with both B and C considered for a different scaffold. A maximum links ratio of 1 (not recommended) means that the best two candidate contig pairs have the same number of links -- SSPACE will accept the first one since both have a valid gap/overlap. The above method was adopted from SSAKE. The SSPACE improved this method by introduing another method if a contig can link to more than one alternative. Both methods (original SSAKE method and our method) for handling alternatives are explained below;
-
-In version 2-0 of SSPACE an additional ratio is used to generate more reliable scaffolds, especially for libraries with large libraries. This ratio is used as an additional control for the scaffolding process. A contig with multiple links should satisfy both ratios in order to form a scaffold. The rules for scaffolding contigs with multiple alternative contig connections is explained in more detail below.
-
-If a contig can be linked to more than one alternative, connections between these alternatives are searched and linked together if a connection is found. Otherwise a ratio is calculated between the two best alternatives. If this ratio is below a threshold (-a) a connection with the best scoring alternative is established. The two methods are shown below;
-
-The first method;
-A has 10 links with B
-A has 5 links with C
-B has 10 links with C;
-
-Result is a scaffold containing A-B-C
-
-The second method (only used if first method did not produce a scaffold) is based on two ratios. The first ratio (ratio1) is based on the number of links, while the second ratio (ratio2) is based on the number of links and the used search space. This will be explained using an example;
-
-If we have an insert size of 450 and contigs has two alternatives with two contigs, with the following details;
-
-A and B with;
- gap = 100
- links = 19
- size of B is 100bp
-
-A and C with;
- gap = 400
- links = 9
- size of B is 1000bp
-
-Ratio1 is simply calculated by dividing the contig with lowest links with the contig with highest number of links;
-
-Here, this is 9/19 (C/B) = 0.47.
-
-
-Ratio2 is calculated by incorporating the insert size. SSPACE first determines the amount of search space that was used for searching links.
-
-In figure, where each character represents 50bp, this looks something like;
-
- <100bp>
- ==(B)
-gap=100 /
- /
-(A)======
- \
-gap=400 \
- ------====================(C)
- <1000bp>
- *********
- < SEARCH SPACE >
-
-Legenda;
-* = search space
-= = contig
-- = gap
-
-Now we calculate the used space on contigs (B) and (C) that was used for pairing with contig (A). In principle, this is just calculating the number of nucleotides fall into the SEARCH SPACE.
-For contig B, we can see that the whole contig falls into the SEARCH SPACE. Therefore, the space = 100bp
-For contig C, we can see that only the first 50bp of the contig falls into the SEARCH SPACE. Therefore, the space = 50bp.
-
-Next, we estimate the number of links per space, by dividing the total number of links with the found space;
-For contig B, this is 19 links per 100 bp space = 0.19 links per space
-For contig C, this is 9 links per 50 bp space = 0.18 links per space
-
-Ratio2 is then calculated by dividing the two numbers; 0.18/0.19 = 0.95. If both ratio1 and ratio2 are below the -a ratio threshold, the scaffold is A-B. Otherwise, no reliable scaffold can be formed and the scaffold extension is stopped.
-
-5b. Left scaffold extension
-When a scaffold extension is terminated on one side, the scaffold is extended on the "left", by looking for contig pairs that involve the reverse of the seed (in this example, rD). With AB and AC having 4 and 2 links, respectively and rD being the only pair on the left, the final scaffolds outputted by SSPACE would be:
-
-1) rD-A-B
-2) C
-
-SSPACE outputs a .scaffolds file with linkage information between contigs (see "Understanding the .scaffolds csv file" below)
-Accurate scaffolding depends on many factors. Number and nature of repeats in your target sequence, optimum adjustments of insert size, error, parameters -k and -a and data quality/size of sequence set (more doesn't mean better) will all affect SSPACE's ability to build scaffolds.
-
-
-6. Merging contigs
-SSAKE scaffolder produces links between contigs and determines the possible gap between them. For a positive gap, m number of N's will be placed between them if a gap of size m is predicted to occur. When a negative gap is generated, a putative overlap is predicted to occur. The adjacent contigs are searched for overlap within a window given at -n option till 50 bp. If an overlap was found, contigs are merged and the region is marked with lowercase nucleotides. Otherwise, if no overlap was detected, a single "n" will be placed between the contigs. A short overview of this step with three examples;
-
->contig_1
-AGCTAGTCGTAGCTTGTAC
->contig_2
-ACGTAGTGATATTATTGTC
-
-Example 1:
-A link between contig_1 and contig_2 is found, with a putative gap of 10. In the final output, the gaps is indicated by 10 N's between the two contigs.
-
-Link = contig_1 with contig_2. Gap = 10;
-AGCTAGTCGTAGCTTGTACNNNNNNNNNNACGTAGTGATATTATTGTC
-
-Example 2;
-A link between contig_1 and contig_2 is found, with a putative gap of -10. When using the -n 10 option, no overlap was found and a small <n> is inserted between the two contigs.
-
-Link = contig_1 with contig_2. Gap = -10. -n = 10;
-AGCTAGTCGTAGCTTGTACnACGTAGTGATATTATTGTC
-
-Example 3;
-A link between contig_3 and contig_4 is found, with a putative gap of -10. When using the -n 10 option, an overlap of 13 nucleotides was found, indicated in lower case in the final output.
-
->contig_3
-AGTGTTAGATAGTTATAGA
->contig_4
-AGATAGTTATAGAAGTAGT
-
-Link = contig_3 with contig_4. Gap = -10. -n = 10;
-AGTGTTagatagttatagaAGTAGT
-
-TIP: The summary file calculates the mean and median insert size based on mapping of paired reads on a single contig. For more reliable gap and overlap estimation, one may consider to change the insert size in the library file with the calculated mean.
-
-
-Input sequences
----------------
-
-FASTA FILES:
->ILLUMINA-52179E_0001:3:1:1062:15216#0/2
-ATNGGGTTTTTCAACTGCTAAGTCAGCAGGCTTTTCACCCTTCAACATC
->ILLUMINA-52179E_0001:3:1:1062:4837#0/2
-ANNAACTCGTGCCGTTAAAGGTGGTCTTGCATTTCAGAAAGCTCACCAG
-
-FASTQ files:
-@ILLUMINA-52179E_0001:3:1:1062:15216#0/2
-ATNGGGTTTTTCAACTGCTAAGTCAGCAGGCTTTTCACCCTTCAACATC
-+ILLUMINA-52179E_0001:3:1:1062:15216#0/2
-OOBOLJ[HHO`_aaa`a_]aaaY[`Za[Y[F]]VZWX]WZ^Z^^^O[XY
-@ILLUMINA-52179E_0001:3:1:1062:4837#0/2
-ANNAACTCGTGCCGTTAAAGGTGGTCTTGCATTTCAGAAAGCTCACCAG
-+ILLUMINA-52179E_0001:3:1:1062:4837#0/2
-OBBOO^^^^^bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb`bbbb`
-
-General points:
--Files present in the -l library file should either be in .fastA or .fastQ format, which is automatically determined by the program. For each paired read, one of the reads should be in the first file, and the other one in the second file. The paired reads are required to be on the same line in both files.
--the header (given after "@" character for .fastaQ or ">" for .fastaA) of contig and paired-read data files could be of any format. No typical naming convention is needed. Duplicate names are also allowed.
--Quality values of the fastQ files are not used.
--To be considered, sequences have to be longer than 16 nt or -m (but can be of different lengths). If they are shorter, the program will simply omit them from the process.
--Reads containing ambiguous bases, like <N> and <.>, and characters other than ACGT will be ignored entirely in input fasta/fastaq files inserted with -l option.
--Contigs (inserted with -s option) containing ambiguous bases, like <N> and <.>, and characters other than ACGT are not ignored. However, contigs having these other characters can prevent proper contig extension when they are at the beginning or end of the sequence.
--Spaces in any .fastq and .fasta file are NOT permitted and will either not be considered or result in execution failure
--For Bowtie, option -v 0 is used, which correspond to zero mismatches allowed on mapping. In addition bowtie's -m 1 option is used; only reads that map exactly to one contig (both in normal and reverse complement) are outputted. Pairs that are present on multiple contigs, are not used for scaffolding. Results are stored in the folder 'bowtieoutput'. For information about Bowtie see (bowtie-bio.sourceforge.net/).
-
-
-Fasta header of .extendedcontig.fasta file
-------------
-
-e.g.
->extcontig27|size52|read193|cov92.79|seed:PreAssembledCtg0027
-
-contig id# = 27, this contig is extended during extension step. If not extended, the contig is named >contig27
-size (G) = 52 nt. Size of the contig.
-number of reads (N) = 193. Number of reads for extension.
-cov [coverage] (C) = 92.79. the coverage (C) is calculated using the total number (T) of consensus bases [sum(L)] provided by the assembled sequences divided by the contig size:
-
-C = T / G
-seed = PreAssembledCtg0027. Header of the original pre-assembled contig file.
-
-Output files
-------------
-Each file is starting with a basename given at the -b parameter. First, four main files are generated in the current working directory;;
-
-(basename).final.scaffolds.fasta :: text file; Final scaffolds produced by SSPACE.
-(basename).final.evidence:: text file; Produced scaffolds including the initial numbered contigs.
-(basename).logfile :: text file; Logs execution time / errorsE
-(basename).summaryfile:: text file; Gives a summary after every step. Summary of number of inserted sequences, filtered sequences, contig sequences, mapping stats, pairing stats and contig/scaffold size summaries.
-
-
-In addition, four folders are generated, each having a number of files;
-
-'reads' folder;
-(basename).(libname).file(libnumber).fasta:: fasta file; Converted files of the paired-read data, each two consecutive sequences are pairs. This file is used as input for both the contig extension as the scaffolding step..
-
-'bowtieoutput' folder;
-Four files are generated by bowtie;
-(basename).bowtieIndex.* :: index file; Index files generated by 'bowtie-build'. Produced for each library.
-
-For further information about the outputs of Bowtie, see the Bowtie manual (bowtie-bio.sourceforge.net/).
-
-
-'pairinfo' folder;
-(basename) .(libname).pairing_distribution.csv:: comma-separated file; 1st column is the calculated distance for each pair (template) with reads that assembled logically within the same contig. 2nd column is the number of pairs at that distance. Produced for each library.
-(basename).(libname).pairing_issues:: text file; Lists all pairing issues encountered between contig pairs and illogical/out-of-bounds pairing. Produced for each library.
-
-'intermediate_results' folder;
-(basename).extendedcontigs.fasta :: fasta file; All contig sequences. Both extended and non-extended contigs. Extended contigs are named ">ext_contig" , while non-extended are named ">contig" in the header. Only produced when -x 1.
-
-(basename).formattedcontigs.fasta :: fasta file; Original contig sequences. Formatted to appropriate input for scaffolding. Only produced when -x 0.
-
-(basename).(libname).scaffolds :: comma-separated file; see below. Produced for each library.
-
-(basename).(libname).scaffolds.fasta :: fasta file; All merged/unmerged contigs within scaffolds are listed. The overlap sequence between contigs (>= -n bases) will be shown in lower case within the merged contig. Note that *perfect* sequence overlap has to occur between 2 predicted adjacent contigs of a scaffold in order to merge. Only merging of two contigs is established if a negative gap is determined. When two consecutive contigs do not physically overlap, then gaps will be padded with Ns of length corresponding to the predicted gap size m (refer to Understanding the .scaffolds csv file below) and predicted but undetected overlaps with a single (n).
-
-(basename).(libname).scaffolds.evidence :: text file; Produced scaffolds including the initial numbered contigs (-s option). (refer to Understanding the .evidence file below).
-
-(basename).(libname).foundlinks :: text file; Links between the contigs/scaffolds and their correspond gapsize.
-
-(basename).(libname).repeats :: text file; Contig-edges having multiple links with other contigs.
-
-
-'dotfiles' folder;
-(basename).(libname).visual_scaffolds.dot :: dot file; This file can be used to visualise the contigs orientation and order on the scaffolds. The .dot file can be converted to any format using the GraphViz package using the 'dot' command (www.graphviz.org). Each dotfile is cut into 5mb parts, otherwise the scaffolds can't be converted and visualised properly.
-
-
-Understanding the .scaffolds csv file
--------------------------------------
-
-scaffold1,7484,f127Z7068k12a0.58m42_f3090z62k7a0.14m76_f1473z354
-
-Each column is separated by a comma;
-column 1: a unique scaffold identifier
-column 2: the sum of all contig sizes that made it to the scaffold/supercontig
-column 3: a contig chain representing the layout:
-
-e.g.
-f127Z7068k12a0.58m42_f3090z62k7a0.14m76_f1473z354
-
-means: contig f127 (strand=f/+), size (z) 7068 (Z if contig was used as the seed sequence) has 12 links (k), link ratio of 0.58 (a) with a mean gap of 42nt (m) with reverse (r) of contig 3090 (size 62) on the right. if m values are negative, it's just that a possible overlap was calculated using the mean distance supplied by the user and the position of the reads flanking the contig.
-Negative m values imply that there's a possible overlap between the contigs. But since the pairing distance distribution usually follows a Normal/Gaussian distribution, some distances are expected to be larger than the median size expected/observed. In reality, if the exact size was known between each paired-reads, we wouldn't expect much negative m values unless a break occurred during the contig extension (likely due to base errors/SNPs).
-
-
-
-Understanding the .scaffolds.fasta file
-
--------------------------------------
-
-scaffold13.1|size84140|tigs14
-
-Each column represents;
-name of the scaffold
-size of the scaffold
-number contigs in scaffold
-
-Each initial contig inputted at -s option stored in a scaffold is written to the .evidence file. This file is explained below.
-
-Understanding the .scaffolds.evidence file
--------------------------------------
-
->scaffold1.1|size9058|tigs5
-f_tig5|size728|links12|gaps100
-r_tig1|size2726|links10|gaps89
-f_tig100|size3687|links4|gaps-46|merged40
-f_tig91|size238|links6|gaps392
-f_tig120|size1112
-
-The first line indicates the scaffold, which is the same as in the .scaffolds.fasta file. Next, for each contig the connection (orientation, links and gaps) with other contigs are given. The second line for example means forward contig 5 with size 728 has 12 links and a gap of 100bp with reverse contig 1. If a line ends with <merged>, it means that the contig has overlap with the next contig, and they are merged. For contig f_tig100, 40 nucleotides had an overlap with contig f_tig91.
-
-
-Producing visualisation of scaffolds with .dot file using -p parameter
--------------------------------------
-To visualize the scaffolds of the .dot file, GraphViz should be downloaded at (www.graphviz.org). GraphViz converts the .dot file to any desired output using the 'dot' function. For example to convert the .dot to a .ps format;
-
-dot -Tps2 (basename).(libname).visual_scaffolds.dot -o MYOUTPUT.ps
-
-This will produce a postscript (.ps) file. For other options, see the manual of GraphViz.
-
-
-
-How does the .tab file work
--------------------------------------
-The .tab file is a tab-delimited file containing information about the positions of the reads on the contigs. On each line, positions of both reads are given.
-
-A typical .tab file line looks like;
-
-contig1 100 150 contig1 300 250
-
-Here, the first read is found at contig1 with start and end at position 100 and 150, respectively. Meaning that the read is found at the positive strand (-).
-The second read is found at contig1 at start and end at position 300 and 250, respectively. Meaning that the read is found at the negative strand (-).
-
-In figure;
- read1 read2
- ----> <----
-contig1 ----------------------------------------------------
-
-
-Another line may look like;
-
-contig2 300 350 contig3 100 550
-
-Here, the first read is found at contig1 with start and end at position 100 and 150, respectively. Meaning that the read is found at the positive strand (-).
-The second read is found at contig1 at start and end at position 300 and 250, respectively. Meaning that the read is found at the negative strand (-).
-
-In figure;
- read1
- ----> read2
-contig2 ------------------------ <----
-contig3 -------------
-
-Normally, SSPACE parses the output of Bowtie directly to the above format and uses this information to pair the contigs and to determine the insert size. With the .tab format, users can put directly the mapping positions of the reads into SSPACE, which is much faster. Also, this way users can make use of their favorite read mapper and put the results into SSPACE.
-
-To work properly, the input contigs (-s option) should have the same name as the contigs in the .tab file, as explained in the MANUAL. Since the TAB file can be used in combination with other TAB files and also fasta/fastq files, as well as multiple libraries, the original mappings should be updated after each library. Therefore, contigs are stored in memory, and their position in scaffolds is updated after each scaffold formation. An example;
-
-contig2 (200bp) is linked with contig3 (200bp) with a gap of 10bp
-
- contig3 contig2
-scaf1------------------------NNNNNNNNNN--------------
-
-the contigs are then updated to new positions;
--contig3 is at position 1-200 at scaf1
--contig2 is at position 210-410 at scaf1
-
-Most common used output format of read mappers are .sam format and their equivalent binary format .bam. A script is attached in the 'tools' folder in the SSPACE package, which converts .sam/.bam files to .tab format. See the TUTORIAL on an example on how such a process looks like.
-
-SSPACE does not
---------------
-
--Take into consideration base quality scores. It is up to the user to process the sequence data before clustering with SSPACE. Python scripts (TQS.py, TQSfastq.py, TQSexport.fq) are provided to help trim poor quality bases off Illumina sequences. Refer to TQS.readme and TRIMMING_PAIRED_READS.README included in this distribution (in the ./tools subdirectory) for information on how to run those programs
--Consider sequence read having any character other than A,C,G,T and will skip these reads entirely while reading the fasta file.
--Only input of .fasta or .fastq is possible. For conversion to these formats use the fq_all2std.pl function in the ./tools directory.
diff --git a/external/gatb-minia-pipeline/sspace/SSPACE_Basic_v2.0.pl b/external/gatb-minia-pipeline/sspace/SSPACE_Basic_v2.0.pl
deleted file mode 100755
index d4ac5890e856c560fbfc1106d9b5e0b176b90bbe..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/SSPACE_Basic_v2.0.pl
+++ /dev/null
@@ -1,665 +0,0 @@
-#!/usr/bin/perl
-
-#AUTHOR
-# Marten Boetzer and Walter Pirovano (c) 2010
-# SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension (SSPACE)
-# walter.pirovano@baseclear.com
-
-#NAME
-# SSPACE Marten Boetzer - Walter Pirovano November 2011
-
-#SYNOPSIS
-# SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension (SSPACE)
-
-#DOCUMENTATION
-# README, MANUAL and TUTORIAL distributed with this software @ www.baseclear.com
-# Boetzer M, Henkel VJ, Jansen HJ, Butler D and Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4) p578-9.
-# http://www.baseclear.com/sequencing/data-analysis/bioinformatics-tools/
-# We hope this code is useful to you -- Please send comments & suggestions to Walter.Pirovano@baseclear.com
-# If you use either the SSPACE code or ideas, please cite our work appropriately and accurately
-
-#LICENSE
-# SSPACE Copyright (c) 2010-2011 BaseClear B.V. The Netherlands. All rights reserved.
-# SSAKE Copyright (c) 2006-2010 Canada's Michael Smith Genome Science Centre. All rights reserved.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# note: insert size and distance between pairing reads are used interchangeably
-
-#MAJOR CHANGES ON SSAKE V3.4 TO FORM SSPACE
-# -New scaffolding feature dealing with contigs having multiple alternatives
-# -Seperate scripts to decrease the memory usage
-# -Automatic filtering of reads and duplicate mate pairs
-# -Option for contig extension on unfiltered reads
-# -Removed tracking of reads during contig extension
-# -Mapping single reads to extended and non extended contigs
-# -Single reads mapped more than once to a contig are removed for scaffolding
-# -A summary file is generated containing detailed information about the scaffolding process
-# -An evidence file is generated which indicates the contigs present in the scaffolds
-# -Optional; Scaffolds and their contigs are visualised by generating a .dot file
-
-#MAJOR CHANGES ON SSPACE Basic v2.0;
-
-# GENERAL
-# -Last column of the library file should be the orientation of the reads, instead of indication of being reverse complement or not. Options are FR, FF, RF and RR.
-# -Fixed some bugs in the summary file and removed some useless information.
-# -Included the -z option which specifies the minimal contig length that will be used for scaffolding. Contigs below this length are discarded for scaffolding.
-# -Included the possibility to include TAB delimited files with read mapping information, format is; ctg1 start1 end1 ctg2 start2 end2
-# - if a read is reverse complement on a contig, start and end should be turned around e.g. ctg1 100 150 ctg2 150 100 indicates that the second read is reverse complement on ctg2
-# - No contig filtering can be applied if TAB delimited files are included
-# - See MANUAL for more information of how to use the tab file option
-# -Included some scripts to convert a .sam file to a .tab file
-
-# BOWTIE
-# -Included the -g option to specify maximum allowed gaps for Bowtie. This option corresponds to the -v option in Bowtie.
-# -Now able to do multithreaded Bowtie using the -T option (-T 3 does 3 threads). This option corresponds to the -p option in Bowtie.
-
-# READING FILES:
-# -Speeded up the reading of the library files for a single threaded run
-# -Now able to read multiple libraries at once using the multithread -T option. -T 3 reads three files at the same time.
-
-# CONTIG EXTENSION
-# -Included the -r option for contig extension (default is 0.9).
-# -Speeded up and reduced the memory usage during the contig extension.
-# - SSPACE reads in the output of Bowtie at once, rather than reading it from the output file.
-# - Faster check for presence of subsequence of a read, thereby able to faster check for overlapping sequences with the contig.
-
-# SCAFFOLDING
-# -Combined the functions readBowtie and pairContigs, which saves runtime and memory.
-# -Saving runtime by reading Bowtie results in at once, instead of reading it from Bowtie's output file.
-# -Included a pre-filtering step of multiple alternative contig links before scaffolding. This step was previously done during scaffolding, now it's a step before scaffolding. It reduces the number of errors within the scaffolds.
-# -Additional check to connect two alternative contigs, making the scaffolds more reliable, especially with mate pair libraries. The search space is included in the calculation of the ratio, rather than looking at the number of links only. See the README file for more information.
-# -Calculation of mean insert size based on mapped read pairs on same contig. Users can choose this value for better estimation of gap sizes. Especially for paired-end sequences.
-
-# -Fixed a bug in the mergeContigs function. Indication of contigs merged in previous libraries were not displayed in the final .evidence file.
-
-#-------------------------------------------------LOAD PACKAGES AND DEFINE VARIABLES
- use strict;
- use Storable;
- require "getopts.pl";
- use File::Path;
- use File::Basename;
-
- #Specify path to DotLib
- use FindBin qw($Bin);
- use lib "$Bin/dotlib/";
- use DotLib;
-
- use vars qw($opt_m $opt_o $opt_v $opt_p $opt_k $opt_a $opt_z $opt_s $opt_b $opt_n $opt_l $opt_x $opt_u $opt_t $opt_T $opt_g $opt_r);
- &Getopts('m:o:v:p:k:a:z:s:b:n:l:x:u:t:T:g:r:');
- my ($base_overlap,$min_overlap,$verbose,$MIN_READ_LENGTH,$SEQ_SLIDE,$min_base_ratio,$min_links,$max_link_ratio,$unpaired_file,$max_trim,$base_name, $max_count_trim,$min_tig_overlap, $doplot, $extending, $threads, $minContigLength, $gaps, $unpaired,$gapclosure)= (20, 32, 0, 16, 1, 0.9, 5, 0.70, "no-u", 0, "standard_output", 10, 15, 0, 0, 1, 0, 0, 0,0);
-
- my $version = "[SSPACE_Basic_v2.0_linux]";
- my $seplines = ("-" x 60)."\n";
- my ($MAX, $MAX_TOP, $TRACK_COUNT) = (0, 100, 1);# $MAX_TOP is the very maximum anchoring edge sequence that will be searched
-
-#-------------------------------------------------READ OPTIONS
-
- if(!($opt_l) || !($opt_s)){
- print "ERROR: Parameter -l is required. Please insert a library file\n" if(!$opt_l);
- print "ERROR: Parameter -s is required. Please insert a contig .fasta file\n" if(!$opt_s);
- print "\nUsage: $0 $version\n\n";
-
- print "============ General Parameters ============\n";
- print "-l Library file containing two mate pate files with insert size, error and either mate pair or paired end indication.\n";
- print "-s Fasta file containing contig sequences used for extension. Inserted pairs are mapped to extended and non-extended contigs (REQUIRED)\n";
- print "-x Indicate whether to extend the contigs of -s using paired reads in -l. (-x 1=extension, -x 0=no extension, default -x 0)\n";
- print "============ Extension Parameters ============\n";
- print "-m Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m $min_overlap)\n";
- print "-o Minimum number of reads needed to call a base during an extension (default -o $base_overlap)\n";
- print "-t Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t $max_trim, optional)\n";
- print "-u Fasta/fastq file containing unpaired sequence reads (optional)\n";
- print "============ Scaffolding Parameters ============\n";
- print "-z Minimum contig length used for scaffolding. Filters out contigs that are below -z (default -z 0 (no filtering), optional).\n";
- print "-k Minimum number of links (read pairs) to compute scaffold (default -k $min_links, optional)\n";
- print "-a Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a $max_link_ratio, optional)\n";
- print "-n Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -n $min_tig_overlap, optional)\n";
- print "============ Bowtie Parameters ============\n";
- print "-T Specify the number of threads in Bowtie. Corresponds to the -p/--threads option in Bowtie (default -T $threads, optional)\n";
- print "-g Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the -v option in Bowtie. *higher number of allowed gaps can lead to least accurate scaffolding* (default -v 0, optional)\n";
- print "============ Additional Parameters ============\n";
- print "-b Base name for your output files (optional)\n";
- print "-v Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)\n";
- die "-p Make .dot file for visualisation (-p 1=yes, -p 0=no, default -p 0, optional)\n";
-
- }
-
- my $filecontig = $opt_s if($opt_s);
- $min_overlap = $opt_m if ($opt_m);
- $base_overlap = $opt_o if ($opt_o);
- $threads = $opt_T if ($opt_T);
- $verbose = $opt_v if ($opt_v);
- $min_links = $opt_k if ($opt_k);
- $max_link_ratio = $opt_a if ($opt_a);
- $min_base_ratio = $opt_r if ($opt_r);
- $base_name = $opt_b if($opt_b);
- $min_tig_overlap = $opt_n if($opt_n);
- $unpaired_file = $opt_u if($opt_u);
- $doplot = $opt_p if($opt_p);
- $extending = $opt_x if($opt_x eq 1);
- $minContigLength = $opt_z if($opt_z);
- $gaps = $opt_g if($opt_g);
- my $libraryfile;
- $libraryfile = $opt_l if ($opt_l);
-
-#-------------------------------------------------CHECKING PARAMETERS
- die "ERROR: Invalid (-l) library file $libraryfile ...Exiting.\n" if(! -e $libraryfile);
- die "ERROR: Invalid (-s) contig file $filecontig ...Exiting.\n" if(! -e $filecontig);
- die "ERROR: -x must be either 0 or 1. Your inserted -x is $extending...Exiting.\n" if(!($extending == 0 || $extending == 1));
- die "ERROR: -m must be a number between 15-50. Your inserted -m is $min_overlap ...Exiting.\n" if(!($min_overlap =~ /^\d+$/) || $min_overlap < 10 || $min_overlap > 50);
- die "ERROR: -o must be set to 1 or higher. Your inserted -o is $base_overlap ...Exiting.\n" if($base_overlap < 1);
- die "ERROR: -k must be an integer number. Your inserted -k is $min_links ...Exiting.\n" if(!($min_links =~ /^\d+$/));
- die "ERROR: -a must be a number between 0.00 and 1.00. Your inserted -a is $max_link_ratio ...Exiting.\n" if($max_link_ratio < 0 ||$max_link_ratio > 1);
- die "ERROR: -n must be an integer number. Your inserted -n is $min_tig_overlap ...Exiting.\n" if (!($min_tig_overlap =~ /^\d+$/));
- die "ERROR: Invalid unpaired file $unpaired_file -- fatal\n" if(! -e $unpaired_file && $opt_u);
- die "ERROR: -p must be either 0 or 1. Your inserted -p is $doplot...Exiting.\n" if(!($doplot == 0 || $doplot == 1));
- die "ERROR: -z must be positive integer. Your inserted -z is $minContigLength...Exiting.\n" if (!($minContigLength =~ /^\d+$/));
- die "ERROR: -g must be positive integer between 0 and 3. Your inserted -g is $gaps...Exiting.\n" if (!($gaps =~ /^\d+$/) || $gaps > 3);
- die "ERROR: -T must be positive integer. Your inserted -T is $threads...Exiting.\n" if (!($threads =~ /^\d+$/));
-
-#-------------------------------------------------check library file;
- open(FILELIB, "< $libraryfile");
- my ($min_allowed, $library, $fileA, $fileB, $insert_size, $insert_stdev, $orientation);
- my $countline=0;
- while(<FILELIB>){
- chomp;
- $countline++;
- my @line = split(/\s+/, $_);
- if($#line >= 0){
- if($opt_l){
- die "ERROR: Line $countline in your library file ($libraryfile) contains $#line spaces, which should be 5 spaces. Check that no spaces are within the file names.\n" if($#line != 5);
-
- my ($library, $fileA, $fileB, $insert_size, $insert_stdev, $orientation) = split(/\s+/, $_);
- if($fileA ne "TAB"){
- die "ERROR: Invalid file in library $library: $fileA -- fatal\n" if(! -e $fileA);
- }else{
- die "ERROR: Can't apply filtering using the -z option (-z = $minContigLength)and insertion of a TAB file -- fatal\n" if($minContigLength > 0);
- }
- die "ERROR: Invalid file in library $library: $fileB -- fatal\n" if(! -e $fileB);
- die "ERROR: Insert size should be higher than or equal to 0. Your library $library has insert size of $insert_size. Exiting.\n" if(!($insert_size>0) || !($insert_size =~ /^\d+$/));
- die "ERROR: Insert stdev must be a number between 0.00 and 1.00. Your library $library has insert size of $insert_stdev. Exiting.\n" if($insert_stdev < 0 || $insert_stdev > 1 || !($insert_stdev * 1 eq $insert_stdev));
- die "ERROR: Orientation must have length of 2 characters and should contain one of the following; FR, FF, FR or RF. Your library $library has orientation of $orientation ...Exiting.\n" if(!(length($orientation) == 2) || !($orientation =~ /[FR][FR]/));
- }
- }
- }
- close FILELIB;
-#-------------------------------------------------Make folder structure
- mkpath('intermediate_results');
- mkpath('pairinfo');
- mkpath('reads');
- mkpath('bowtieoutput');
-
- $unpaired = $unpaired_file if (-e $opt_u && $extending == 1);
-#-------------------------------------------------Print input parameters
- my $contig = "intermediate_results/" . $base_name . ".formattedcontigs.fasta";
-
- my $log = $base_name . ".logfile.txt";
- my $summaryfile = $base_name.".summaryfile.txt";
- open (LOG, ">$log") || die "Can't write to $log -- fatal\n";
-
- open (SUMFILE, ">$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- close SUMFILE;
-
- my $init_message = "Your inserted inputs on $version at ".getDate().":\nRequired inputs: \n\t-l = $libraryfile\n\t-s = $filecontig\n\t-b = $base_name\n\n";
- $init_message .= "Optional inputs:\n\t-x = $extending\n\t-z = $minContigLength\n\t-k = $min_links\n";
- $init_message .= "\t-a = $max_link_ratio\n\t-n = $min_tig_overlap\n\t-T = $threads\n\t-p = $doplot\n\n";
-
- $init_message .= "Contig extension inputs:\n\t-o = $base_overlap\n\t-t = $max_trim\n\t-m = $min_overlap\n\t-r = $min_base_ratio\n\n" if($extending == 1);
-
- &printMessage($init_message);
- close LOG;
-#-------------------------------------------------READING AND CONVERTING INPUT SEQUENCES
- system("perl $Bin/bin/readLibFiles.pl $libraryfile $base_name $extending $unpaired $min_overlap $threads");
- checkStatus();
-#-------------------------------------------------FORMATTING OR EXTENDING CONTIGS
- system("perl $Bin/bin/ExtendOrFormatContigs.pl $contig $base_name $extending $filecontig $MIN_READ_LENGTH $base_overlap $min_overlap $min_base_ratio $max_trim $verbose $Bin $minContigLength $libraryfile $gaps $threads");
- checkStatus();
-#--------------------------------------------------UPDATE SUMMARY FILE
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- open (LOG, ">>$log") || die "Can't write to $log -- fatal\n";
-
- #write summary of initial contigs
- my $sumfile .= "\nSUMMARY: \n".$seplines."\tInserted contig file;\n";
- $sumfile = &writesummaryfiles($filecontig, "contig", $sumfile);
- #write summary of extended contigs
- my $extended_tig = "intermediate_results/" . $base_name . ".extendedcontigs.fasta";
- $sumfile .= "\tAfter extension;\n" if($extending);
- $sumfile = &writesummaryfiles($extended_tig, "contig", $sumfile) if($extending);
-
- #write summary of filtered contigs
- if($minContigLength > 0){
- $sumfile .= "\tAfter filtering (z >= $minContigLength);\n";
- $sumfile = &writesummaryfiles($contig, "contig", $sumfile);
- }else{
- $contig = $extended_tig if($extending);
- }
- &FlushFiles();
- close LOG;
- close SUMFILE;
-
-#--------------------------------------------------GO THROUGH EACH LIBRARY AND SCAFFOLD
- open(FILELIB, "< $libraryfile") || die "Can't open $libraryfile -- fatal\n";
- my ($lib, $fileA, $fileB, $insert_size, $insert_stdev, $pair, $headscaffolds, $prevlib, $mergedtigs, $evidencefile);
-
- while(<FILELIB>){
- chomp;
- &FlushFiles();
- ($lib, $fileA, $fileB, $insert_size, $insert_stdev, $orientation) = split(/\s+/, $_);
- next if($lib eq $prevlib || $lib eq '');
-
- my $tabfile = 0;
- $tabfile = 1 if($fileA eq "TAB");
-
- $prevlib = $lib;
- $min_allowed = -1 * ($insert_stdev * $insert_size);
-
- open (LOG, ">>$log") || die "Can't write to $log -- fatal\n";
- &printMessage("\nLIBRARY $lib\n".$seplines);
- close LOG;
-
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- print SUMFILE "\n\nLIBRARY $lib STATS:\n".("#" x 80),"\n";
- close SUMFILE;
-
- my $scaffold = "intermediate_results/" . $base_name . ".$lib.scaffolds";
- $mergedtigs = "intermediate_results/" . $base_name . ".$lib.scaffolds.fasta";
- my $issues = "pairinfo/" . $base_name . ".$lib.pairing_issues";
- my $distribution = "pairinfo/" . $base_name . ".$lib.pairing_distribution.csv";
-
-#-------------------------------------------------MAPPING READ PAIRS USING FILTERED FASTA FILE
- mkpath("tmp.$base_name");
-#-------------------------------------------------Scaffold the contigs and generate .scaffold file
- system("perl $Bin/bin/PairingAndScaffolding.pl $Bin $gaps $contig $base_name $issues $distribution $verbose $lib $insert_size $min_allowed $scaffold $min_links $max_link_ratio $orientation $threads") if(!$tabfile);
- system("perl $Bin/bin/PairingAndScaffolding.pl $Bin $gaps $contig $base_name $issues $distribution $verbose $lib $insert_size $min_allowed $scaffold $min_links $max_link_ratio $orientation $threads $tabfile $fileB $filecontig $evidencefile") if($tabfile);
- checkStatus();
-
- #retrieve the contigs that were stored
- my $contigstored = "tmp.$base_name/contigs.stored";
- my $contigs = retrieve("$contigstored");
-#-------------------------------------------------Generate .fasta file and .evidence file with scaffolds
- open (LOG, ">>$log") || die "Can't write to $log -- fatal\n";
- ($headscaffolds, $evidencefile) = &mergeContigs($scaffold, $contigs, $mergedtigs, 50, $verbose, $min_tig_overlap,$max_count_trim);
- $contig = $mergedtigs;
-#-------------------------------------------------write summary of scaffolds
- $sumfile .= "\tAfter scaffolding $lib:\n";
- $sumfile = &writesummaryfiles($mergedtigs, "scaffold", $sumfile);
-
-#-------------------------------------------------
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- print SUMFILE ("#" x 80),"\n";
- close SUMFILE;
- &printMessage("\n$seplines");
- $contigs = (''); undef $contigs;
-
- my $removedir = "tmp.$base_name";
- rmtree([$removedir, 'blurfl/quux']); #remove 'tmp' folder
- }#END OF LIBRARY LOOP
-
- #-------------------------------------------------END OF LIBRARIES. PRINT SUMMARY TO FILE AND END SESSION
- my $finalfile = $base_name . ".final.scaffolds.fasta";
- my $finalevfile = $base_name . ".final.evidence";
-
- open (EVID, $evidencefile);
- open (FINALEV, "> $finalevfile");
- while(<EVID>){
- print FINALEV $_;
- }
-
- open (SCAF, $mergedtigs);
- open (FINAL, "> $finalfile");
- while(<SCAF>){
- print FINAL $_;
- }
-
- #make .dot file for visualisation
- &visualiseScaffolds($base_name.".visual_scaffolds", $evidencefile) if($doplot);
-
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- &printMessage("\n=>".getDate().": Creating summary file\n");
- print SUMFILE $sumfile.$seplines;
- my $time = (time - $^T);
- my $minutes = int ($time / 60);
- $time = $time % 60;
- &printMessage(("*" x 50)."\n\nProcess run succesfully on ".getDate()." in $minutes"." minutes and $time"." seconds\n\n\n");
- close SCAF;
- close FINAL;
- close EVID;
- close FINALEV;
- close LOG;
- close SUMFILE;
- #END OF MAIN PROGRAM
-
-###MAKE A .FASTA FILE OF THE FOUND SCAFFOLDS. EITHER MERGE TWO CONTIGS WHEN A OVERLAP OF -n EXISTS OR PLACE A GAP
-sub mergeContigs{
-
- my ($scaffold, $contigs, $mergedtigs, $chunk, $verbose,$min_tig_overlap,$max_count_trim) = @_;
-
- &printMessage("\n=>".getDate().": Merging contigs and creating fasta file of scaffolds\n");
-
- open(IN,$scaffold) || die "can't read $scaffold -- fatal\n";
-
- my $evidence_file = $mergedtigs;
- $evidence_file =~ s/.fasta/.evidence/;
- open(SCAFS,">$evidence_file") || die "can't write to $evidence_file -- fatal\n";
- open(OUT,">$mergedtigs") || die "can't write to $mergedtigs -- fatal\n";
- my $scafhashcount = keys ( %$headscaffolds );
- my $scaffoldHashStart;
- my ($tot,$sct,$ct_merge, $step) = (0,0,0,100);
- while(<IN>){### each line is a scaffold
- chomp;
- my @a = split(/\,/);
- my @tig;
-
- if($a[2]=~/\_/){
- @tig = split(/\_/,$a[2]);
- }else{
- push @tig, $a[2];
- }
- if(++$sct == $step){
- CounterPrint($sct);
- $step = $step + 100;
- }
- my ($ct,$tigsum,$mct,$prev,$word,$template,$seq,$prevseq,$headconcat,$prevEstimatedDistance, $prevLinks) = (0,0,0,"NA","NA","NA","","","","");
- foreach my $t (@tig){### each contig
- $ct++;
-
- if($t=~/([fr])(\d+)z(\d+)(\S+)?/i){
-
- my $orient = $1;
- my $tnum=$2;
- my $head = $orient . $tnum;
- my $search = "tig" . $tnum;
- my $other = $4;
- $tot+= $3;
- $tigsum +=$3;
-
- my ($estimatedDistance, $links) = ("", "");
- $estimatedDistance = $1 if($other=~/m((\-)?\d+)/);
- $links = $1 if($other=~/k((\-)?\d+)/);
- print "\tSC $a[0] - TIG $ct. pattern: $t search: $search totalTigSize: $tot Orientation: $orient Gap/Overlap estimated distance: $estimatedDistance\n" if($verbose);
-
- my $count_trim = 0;
-
- $seq = $contigs->{$tnum}{'seq'};
- $seq = reverseComplement($seq) if($orient eq "r");
- chomp $seq;
- my $prev;
- if($scafhashcount >0){
- $prev = $headscaffolds->{$tnum}{'head'};
- $prev =~ s/^\n//;
- chomp $prev;
- delete $headscaffolds->{$tnum};
- chomp $prev;
- if($orient eq "r"){ ###Reverse all contigs if the whole scaffold is a reverse complement. ftig -> rtig and rtig -> ftig
- my @prevarray = split("\n", $prev);
- if($#prevarray >=0){
- my $newprev="";
- my ($tnum, $sizetig, $links, $gap, $prevline, $merge) = ("","","","","","");
- for(my $i = $#prevarray; $i >= 0; $i--){
-
- my @info = split(/\|/, $prevarray[$i]);
- if($#info eq 1){
- ($tnum, $sizetig) = split(/\|/, $prevarray[$i]);
- }else{
- ($tnum, $sizetig, $links, $gap, $merge) = split(/\|/, $prevarray[$i]);
- }
- $tnum =~ tr/fr/rf/;
- if($prevline ne ""){
- $newprev .= $prevline."|".$links."|".$gap."\n" if($merge eq "");
- $newprev .= $prevline."|".$links."|".$gap."|".$merge."\n" if($merge ne "");
- }
- $prevline = $tnum."|".$sizetig;
- }
- $newprev .= $prevline;
- $prev = $newprev;
- }
- }
- }
- else{
- $prev = "$orient"."_$search|size".length($seq);
- }
- $prev .= "|links$links|gaps$estimatedDistance" if($links ne "");
-
-
- #print "$prev\n";
- if($word ne "NA"){
- #####
- if(length($seq)<=$chunk){
- $template = $seq;
- }else{
- $template = substr($seq,0,$chunk);
- }
-
- ##### word search
- my $dynamic_word = $word;
- if($prevEstimatedDistance <= 0){
- SCAN:
- until($template =~ /$dynamic_word/){
- $dynamic_word = substr($dynamic_word,1,length($dynamic_word));
- if(length($dynamic_word) < $min_tig_overlap){
- $count_trim++;
- last SCAN if($count_trim >= $max_count_trim);
- $dynamic_word = substr($word,0,length($word)-$count_trim);
- }
- }
- }
- if($prevEstimatedDistance <= 0 && $seq =~ /^\S{0,$max_count_trim}$dynamic_word(.*)/){### will grab the left-most match which is ok
- my $tail = $1;
- my $all = "ERROR_";
- while($prevseq =~ /^(.*)$dynamic_word/ig){
- $all = $1;
- }
- print "$prevseq **** $all **** WORD:$word *** DWord:$dynamic_word *** COUNTTRIM:$count_trim\n" if($all=~/ERROR/);
-
- $prevseq = $all . lc($dynamic_word) . $tail;
- my $overlap = length($dynamic_word);
- $ct_merge++;
- print "$ct_merge. GROUNDS FOR MERGING ($overlap nt overlap) !!!\n" if($verbose);
- $headconcat .= "|merged$overlap"."\n".$prev;
- }else{
- ### ADDED RLW 5.MAR.2010
- if($prevEstimatedDistance <= 0){
- $prevseq .= "n" . $seq
- }else{
- $prevseq .= ("N" x $prevEstimatedDistance) . $seq;
- }
- $headconcat .= "\n".$prev;
-
- }
- }else{
- $prevseq = $seq;
- $headconcat = "\n".$prev;
- $mct++;
- }
-
- ##### For the next search
- if(length($seq)<=$chunk){
- $word = $seq;
- }else{
- $word = substr($seq,length($seq)-$chunk,$chunk); ### this will be the next word to search with
- }
- $prevEstimatedDistance = $estimatedDistance;
- $prevLinks = $links;
- }#tig regex
-
- }#each tig
- my $scsz = length($prevseq);
- $scaffoldHashStart->{$sct}{'head'} = $headconcat;
-
- my @line = split(/\n/, $headconcat);
- print SCAFS ">$a[0]|size$scsz|tigs".($#line)."$headconcat\n\n";
- print OUT ">$a[0]|size$scsz\n$prevseq\n";
- $prevseq = '';
- }
- close IN;
- close SCAFS;
- close OUT;
- CounterPrint(" ");
- undef $contigs;
- &FlushFiles();
- return ($scaffoldHashStart, $evidence_file);
-}
-###WRITE SUMMARY STATISTICS FOR ALL CONTIGS OR SCAFFOLDS
-sub writesummaryfiles{
- my ($input_file, $insert, $sumfile) = @_;
-
- open (INFILE, $input_file) || die "Can't open input file $input_file.\n";
-
- my ($counter, $sum, $seq, $name, $foundN50, $sumN50, $totalNcount) = (0,0, "","", 0, 0);
- my (@line, @lengths);
- while (<INFILE>) {
- s/\r\n/\n/;
- chomp;
- $seq.= $_ if(eof(INFILE));
- if ($_ =~ /^[>]/ || eof(INFILE)) {
- if($counter > 0){
- push(@lengths, length($seq));
- $sum+= length($seq);
- my $Ncount = () = $seq =~ /[Nn]/g;
- $totalNcount += $Ncount;
- ($seq) = "";
- }
- $counter++;
- }
- else {
- $seq .= $_;
- }
- }
- $counter--;
- my $half_length = $sum/2;
-
- my @lengths2 = reverse sort { $a <=> $b } @lengths;
-
- for(my $i = 0; $i <= $#lengths && $foundN50 == 0; $i++)
- {
- $sumN50 += @lengths2[$i];
- if($sumN50 >= $half_length){
- $foundN50 = @lengths2[$i] if($sumN50 >= $half_length);
- last;
- }
- }
- $sumfile .= "\t\tTotal number of $insert"."s = $counter\n";
- $sumfile .= "\t\tSum (bp) = ". $sum. "\n";
- $sumfile .= "\t\t\tTotal number of N's = $totalNcount\n";
- $sumfile .= "\t\t\tSum (bp) no N's = ". ($sum-$totalNcount)."\n";
- $sumfile .= "\t\tMax $insert size = ". @lengths2[0]."\n";
- $sumfile .= "\t\tMin $insert size = ". @lengths2[$#lengths]."\n";
- $sumfile .= "\t\tAverage $insert size = ".int($sum/$counter)."\n";
- $sumfile .= "\t\tN50 = ". $foundN50. "\n\n";
-
- close (INFILE);
- close OUTFILE;
-
- return $sumfile;
-}
-
-
-###FUNCTION TO GENERATE A VISUALISATION OF THE SCAFFOLDS AND THEIR CONTIGS IN .DOT FORMAT
-sub visualiseScaffolds{
- my ($dotname, $evidence) = @_;
- my ($filext, $sizecutoff) = (1, 5000000);
- mkpath('dotfiles');
- my $filename2 = "dotfiles/$dotname.part".$filext.".dot";
- &printMessage("\n=>".getDate().": Producing .dot file for visualisation\n");
-
- open(IN,$evidence) || die "can't read $evidence -- fatal\n";
- open(DOT, ">$filename2") || die "can't open $filename2 -- fatal\n";
- printHeader(\*DOT, undef);
- my ($prevtig, $prevgap, $prevlinks, $prevratio, $scafcount) = ("","","", "",0);
- while(<IN>){
- chomp;
- my $line = $_;
- my $filesize = -s $filename2;
-
- if ($line =~ /^[>]/){
- endCluster(\*DOT) if($scafcount > 0);
- my $filesize = -s $filename2;
- if($filesize > $sizecutoff){
- printFooter(\*DOT);
- close(DOT);
- $filext++;
- $filename2 = "$dotname.part".$filext.".dot";
- open(DOT, ">$filename2") || die "can't open $filename2 -- fatal\n";
- printHeader(\*DOT, undef);
- }
- $scafcount++;
- $line =~ tr/[>\|]/ /;
- startCluster(\*DOT, $scafcount, "$line");
- ($prevtig, $prevgap, $prevlinks, $prevratio) = ("","","", "");
- }
- elsif($line =~ /^[fr]/){
- my @info = split(/\|/, $line);
- my ($tnum, $sizetig, $links, $gap);
- if($#info eq 1){
- ($tnum, $sizetig) = split(/\|/, $line);
- }else{
- ($tnum, $sizetig, $links, $gap) = split(/\|/, $line);
- }
- my ($orient, $tig) = split(/_/,$tnum);
- my $ori=-1;
- my ($other, $gap2) = split(/gaps/,$gap);
- my ($other, $links2) = split(/links/,$links);
- $ori = 1 if($orient eq "f");
- printNode(\*DOT, $tig, "$tig ($sizetig)", $ori);
- printEdge(\*DOT, $prevtig, $tig, "gap = $prevgap links = $prevlinks", undef) if($prevtig ne "");
-
- $prevtig = $tig;
- $prevgap = $gap2;
- $prevlinks = $links2;
- }
- }
- endCluster(\*DOT) if($scafcount > 0);
- printFooter(\*DOT);
- close(DOT);
- close IN;
-}
-
-
-###FUNCTION TO REVERSE COMPLEMENT A SEQUENCE
-sub reverseComplement{
- $_ = shift;
- tr/ATGC/TACG/;
- return (reverse());
-}
-
-###FUNCTION TO PRINT MESSAGES TO THE SCREEN AND TO THE LOG FILE
-sub printMessage{
- my $message = shift;
- print $message;
- print LOG $message;
-}
-
-###FUNCTION TO GET THE CURRENT DATE
-sub getDate{
- my $date = scalar(localtime);
- return $date;
-}
-
-###PRINTS A COUNTER ON THE SCREEN AND OVERWRITES PREVIOUS LINE
-sub CounterPrint{
- my $countingMessager = shift;
- print "\r$countingMessager";
- $|++;
-}
-
-###FLUSHES THE SUMMARY AND LOG FILE
-sub FlushFiles{
- select((select(SUMFILE), $| = 1)[0]);
- select((select(LOG), $| = 1)[0]);
- $|++;
-}
-#########END MAIN SCRIPT
-
-
-sub checkStatus{
- &printMessage(("*" x 50)."\n\nProcess failed on ".getDate()."\n\n\n"), exit if(!(-d "process_OK"));
- rmtree(["process_OK", 'blurfl/quux']);
-}
diff --git a/external/gatb-minia-pipeline/sspace/benchmark_SSPACE_Basic_v2-0_25juli.doc b/external/gatb-minia-pipeline/sspace/benchmark_SSPACE_Basic_v2-0_25juli.doc
deleted file mode 100755
index dbfdffa63b398aa7fac0ea788d09b3513dfaab8c..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/sspace/benchmark_SSPACE_Basic_v2-0_25juli.doc and /dev/null differ
diff --git a/external/gatb-minia-pipeline/sspace/bin/ExtendOrFormatContigs.pl b/external/gatb-minia-pipeline/sspace/bin/ExtendOrFormatContigs.pl
deleted file mode 100755
index d826d428ea3950b1053a79b0b8ad2f1f8a852c12..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/bin/ExtendOrFormatContigs.pl
+++ /dev/null
@@ -1,411 +0,0 @@
- ###############################################################
- #Marten Boetzer 1-03-2010 #
- #SSPACE perl subscript ExtendOrFormatContigs.pl #
- #This script, based on the the -x parameter; #
- # -Formats the contigs to appropriate format (-x 0) #
- # -Extends the contigs with available unmapped reads (-x 1) #
- ###############################################################
-
- use strict;
- use File::Basename;
- use File::Path;
-
- my ($MAX, $MAX_TOP, $TRACK_COUNT) = (0, 100, 1);
-
- my $seplines = ("-" x 60)."\n";
-
- my $contig = $ARGV[0];
- my $base_name = $ARGV[1];
- my $extending = $ARGV[2];
- my $filecontig = $ARGV[3];
- my $MIN_READ_LENGTH = $ARGV[4];
- my $base_overlap = $ARGV[5];
- my $min_overlap = $ARGV[6];
- my $min_base_ratio = $ARGV[7];
- my $max_trim = $ARGV[8];
- my $verbose = $ARGV[9];
- my $Bin = $ARGV[10];
- my $minContigLength = $ARGV[11];
- my $libraryfile = $ARGV[12];
- my $gaps = $ARGV[13];
- my $threads = $ARGV[14];
-
-
- my $log = $base_name . ".logfile.txt";
- my $summaryfile = $base_name.".summaryfile.txt";
-
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- open (LOG, ">>$log") || die "Can't write to logfile$log -- fatal\n";
- my $filenameOutExt = $base_name . ".singlereads.fasta";
- my ($bin);
- if($extending == 1){
-
- &ExtendContigs($base_name, $filecontig, $filenameOutExt, $Bin);
- print SUMFILE "\n" if($minContigLength > 0);
- &FormatContigs() if($minContigLength > 0);
- }else{
- &FormatContigs();
- }
-
- close SUMFILE;
- close LOG;
-
- mkpath('process_OK');
-#--------------------------------------------------
-
-###EXTEND CONTIGS WITH UNMAPPED READS
-sub ExtendContigs{
- my ($base_name, $filecontig, $filenameOutExt, $Bin) = @_;
- my ($seq);
- #-------------------------------------------------NOW MAP SINGLE READS TO INITIAL CONTIGS FILE.
- my $readfile = "reads/" . $filenameOutExt;
- &getUnmappedReads($filecontig, $readfile);
- #-------------------------------------------------CONTIG EXTENSION USING UNMAPPED PAIRS STORED IN $SET
- &printMessage("\n=>".getDate().": Contig extension initiated\n");
- my $outfileTig = "intermediate_results/" . $base_name . ".extendedcontigs.fasta";
-
- open (TIG, ">$outfileTig") || die "Can't write to $outfileTig -- fatal\n";
- #--------------------------------------------ASSEMBLY START
-
- ASSEMBLY:
- open(IN,$filecontig) || die "Can't open $filecontig -- fatal\n";
- my ($exttig_count, $counter, $NCount, $orig_mer, $prevhead) = (0,0,0,0,'');
- while(<IN>){
- s/\r\n/\n/;
- chomp;
- $seq.= uc($_) if(eof(IN));
- if (/\>(\S+)/ || eof(IN)){
- my $head=$1;
- $orig_mer = length($seq);
- if($seq ne ''){
- $NCount++ if($seq=~/([NX])/i);
- my $start_sequence = uc($seq);
- my $reads_needed = 1; #tracks coverage
- my $total_bases = $orig_mer * $reads_needed;
-
- ($seq, $reads_needed, $total_bases) = doExtension("3", $orig_mer, $seq, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $counter, $max_trim) if($orig_mer >= $MIN_READ_LENGTH && $orig_mer >= $min_overlap);
-
- my $seqrc = reverseComplement($seq);
- ($seqrc, $reads_needed, $total_bases) = doExtension("5", $orig_mer, $seqrc, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $counter, $max_trim) if($orig_mer >= $MIN_READ_LENGTH && $orig_mer >= $min_overlap);
-
- my $leng = length($seqrc);
- my $reversetig = reverseComplement($seqrc); ### return to sequence, as inputted
- if($leng > $orig_mer){ ### commented out: && $start_sequence ne $seqrc && $start_sequence ne $reversetig
- my $cov = $total_bases / $leng;
- printf TIG ">extcontig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter,$leng,$reads_needed,$cov,$reversetig); #print contigs to file
- $exttig_count++;
- }else{
- my $cov = $reads_needed = 0;
- my $singlet_leng = length($start_sequence);
- printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter,$leng,$reads_needed,$cov,$reversetig); #print singlets to file
- }
- }
- CounterPrint(++$counter);
- $prevhead = $head;
- $seq='';
- }else{
- $seq .= uc($_);
- }
- }
- CounterPrint(" ");
- print SUMFILE "\tNumber of contig sequences =".($counter-1). "\n";
- print SUMFILE "\t\tNumber of contigs containing N's (may prevent proper contig extension) = $NCount\n";
-
- print SUMFILE "\tNumber of contigs extended = $exttig_count\n".$seplines;
- close IN;
- $filecontig = $outfileTig;
- if($@){
- my $message = $@;
- &printMessage("\nSomething went wrong running $0 ".getDate()."\n$message\n");
- }
- close TIG;
-}
-
-###STORE CONTIGS TO APPROPRIATE FORMAT WHEN CONTIGS WILL NOT BE EXTENDED
-sub FormatContigs{
- &printMessage("\n=>".getDate().": Storing contigs to format for scaffolding\n");
- open (TIG, ">$contig") || die "Can't write to $contig -- fatal\n";
- open(IN,$filecontig) || die "Can't open $filecontig -- fatal\n";
- my ($counter, $seq, $prevhead, $step) = (0,'','', 100);
- while(<IN>){
- s/\r\n/\n/;
- chomp;
- $seq.= uc($_) if(eof(IN));
- if (/\>(\S+)/ || eof(IN)){
- my $head=$1;
- my $length_seq = length($seq);
- if($seq ne '' && $length_seq >= $minContigLength){
- if(++$counter == $step){
- CounterPrint($counter);
- $step = $step + 100;
- }
- printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter,$length_seq,0,0.00,$seq);
- }
- $prevhead = $head;
- $seq = '';
- }else{
- $seq .= uc($_);
- }
- }
- CounterPrint(" ");
- close IN;
- close TIG;
-}
-
-###EXTEND CONTIGS
-sub doExtension{
-
- my ($direction, $orig_mer, $seq, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $tig_count, $max_trim) = @_;
-
- my $previous = $seq;
- my ($extended, $trim_ct) = (1,0);
-
- if($orig_mer > $MAX){$orig_mer=$MAX;} ### Deals with special cases where the seed sequences are different from the read set (and possibly very large) - goal here is not to increase sequence coverage of seed, but rather to extend it.
-
- TRIM:
- while($trim_ct <= $max_trim){
- while($extended){
-
- my ($pos,$current_reads,$current_bases,$span) = (0,0,0,"");
-
- ### Added 19March08
- if(length($seq) >= $MAX){ # $seq is length of contig being extended -- if larger than largest read, make sure the largest read could align and all subsequent rds.
- $span = $MAX - $TRACK_COUNT;
- }else{
- $span = length($seq) - $TRACK_COUNT;
- }
- my $startspan = $span;
- my $overhang = {};
- my @overlapping_reads = ();
- for (my $x=1;$x <= ($orig_mer * 2);$x++){
- ($overhang->{$x}{'A'},$overhang->{$x}{'C'},$overhang->{$x}{'G'},$overhang->{$x}{'T'}) = (0,0,0,0);
- }
-
- ### COLLECT SEQUENCES
- while ($span >= $min_overlap){ # will slide the subseq, until the user-defined min overlap size
-
- $pos = length($seq) - $span;
- print "MAX:$MAX, SPAN:$span, POS:$pos" if ($verbose);
-
- my $subseq = substr($seq, $pos, $span); #make a sub-sequence of length l-(1..i) for searching
- my $sub = substr($subseq, 0, 10); #grab first 10 nucleotides and get all reads having this subset stored in $bin
- my $subset = $bin->{$sub}; #Will grab everything even the reverse complement ones
- print "####$direction' SEARCH Position:$pos Span:$span - Subseq:$subseq Previous:$previous\n" if ($verbose);
- ### SEARCH -- this cycles through limited k-mer space
- foreach my $pass (keys %$subset){
- my $pos = index($pass, $subseq);
- if($pos==0){
- my $dangle = substr($pass, $pos+length($subseq));
- #can we align perfectly that subseq to another rd start?
- print "\n", "=" x 80, "\n$direction'- FOUND sequence: $pass -> subset: $subseq -> overhang: $dangle\n", "=" x 80, "\n\n" if ($verbose);
-
- # Collect all overhangs
- push @overlapping_reads, $pass; ### all overlapping reads
- my @over = split(//,$dangle);
- my $ct_oh = 0;
-
- foreach my $bz(@over){
- $ct_oh++; ### tracks overhang position passed the seed
- $overhang->{$ct_oh}{$bz} += $bin->{$sub}{$pass};
- print "$ct_oh - $bz = $overhang->{$ct_oh}{$bz}\n" if($verbose);
- }
- }
- }
- $span--;
- }#while overlap >= user-defined -m minimum
-
- my $consensus = "";
- print "Finished Collecting Overlapping Reads - BUILDING CONSENSUS...\n" if ($verbose);
- # print Dumper(@overlapping_reads) if ($verbose);
-
- ### Build consensus
- CONSENSUS:
- foreach my $ohpos (sort {$a<=>$b} keys %$overhang){
- if($ohpos){
-
- my $coverage = $overhang->{$ohpos}{'A'}+$overhang->{$ohpos}{'C'}+$overhang->{$ohpos}{'G'}+$overhang->{$ohpos}{'T'};
- print "pos:$ohpos cov:$coverage A:$overhang->{$ohpos}{'A'} C:$overhang->{$ohpos}{'C'} G:$overhang->{$ohpos}{'G'} T:$overhang->{$ohpos}{'T'}\n" if($verbose);
- if ($coverage < $base_overlap){
- print "COVERAGE BELOW THRESHOLD: $coverage < -o $base_overlap @ $ohpos :: will extend by: $consensus\n" if ($verbose);
- last CONSENSUS;
- }
- my $baselist = $overhang->{$ohpos};
- my ($ct_dna, $previous_bz) = (0, "");
- BASE:
- foreach my $bz (sort {$baselist->{$b}<=>$baselist->{$a}} keys %$baselist){
- if($ct_dna){## the two most abundant bases at that position
- if($previous_bz ne "" && ($baselist->{$previous_bz} / $coverage) >= $min_base_ratio && $baselist->{$previous_bz} > $baselist->{$bz}){### a simple consensus btw top 2
- $consensus .= $previous_bz; ### build consensus
- print "Added base $previous_bz (cov = $baselist->{$previous_bz}) to $consensus **\n" if ($verbose);
- last BASE;
- }else{
- print "ISSUES EXTENDING: best base = $previous_bz (cov=$baselist->{$previous_bz}) at $ohpos. Second-Best: $bz (cov=$baselist->{$bz}) (ratio best=$baselist->{$previous_bz} / total=$coverage) >= $min_base_ratio (-r) -- will terminate with $consensus\n" if($verbose);
- last CONSENSUS;
- }
- }
- $previous_bz = $bz;
- $ct_dna++;
- }
- }
- }
-
- ### deal with sequence reads making up the consensus/newly formed contig
- if($consensus ne ""){
-
- print "Will extend $seq\nwith: $consensus\n\n" if($verbose);
- my $temp_sequence = $seq . $consensus; ## this is the contig extension
- my $integral = 0;
- my $position = length($temp_sequence) - ($startspan + length($consensus));
- my $temp_sequence_end = substr($temp_sequence, $position);
- foreach my $ro (@overlapping_reads){
- if(index($temp_sequence_end, $ro) >= 0){
- $integral=1;
- my $sub = substr($ro, 0, 10);
- $current_reads = $bin->{$sub}{$ro};
- $current_bases = length($ro) * $current_reads;
- $reads_needed += $current_reads;
- $total_bases += $current_bases;
- deleteData($ro);
- }
- }
- if(! $integral){### no reads are found overlapping with the consensus might be indicative of low complexity regions -- Stop the extension
- print "No overlapping reads agree with the consensus sequence. Stopping extension" if ($verbose);
- $extended = 0;
- }else{
- $seq = $temp_sequence;
- $temp_sequence = "";
- print "New Contig is: $seq\n" if ($verbose);
- $extended = 1;
- }
- $previous = $seq;
- }else{### no consensus built, will stop the extension
- $extended = 0;
- }
-
- }###while get the OK for extension
-
- $trim_ct++;
- if ($trim_ct <= $max_trim){
- last TRIM if (length($seq) <= $MIN_READ_LENGTH); #terminate assembly if trimming becomes too agressive
- $seq = substr($seq, 0, -1);
- $extended = 1;
- print "\n$direction prime EXTENSION ROUND $trim_ct COMPLETE UNTIL $max_trim nt TRIMMED OFF => TRIMMED SEQUENCE:$seq\n\n" if ($verbose);
- }
-
- }### while trimming within bounds
-
- print "\n*** NOTHING ELSE TO BE DONE IN $direction prime- PERHAPS YOU COULD DECREASE THE MINIMUM OVERLAP -m (currently set to -m $min_overlap) ***\n\n" if ($verbose);
-
- return $seq, $reads_needed, $total_bases;
-}
-
-
-###DELETE READ DATA IF IT HAS BEEN USED FOR EXTENDING A CONTIG
-sub deleteData {
- my ($sequence) = @_;
-
- my $subnor = substr($sequence, 0, 10);
- my $comp_seq = reverseComplement($sequence);
- my $subrv = substr($comp_seq, 0, 10);
-
- #remove k-mer from hash table and prefix tree
- delete $bin->{$subrv}{$comp_seq};
- delete $bin->{$subnor}{$sequence};
-}
-
-sub getUnmappedReads{
- my ($contigFile, $readfiles) = @_;
- my ($library,$fnames) = ("start","");
-
- #obtain sequences to map against the contigs
- open(FILELIB, "< $libraryfile") || die "Can't open $libraryfile -- fatal\n";
- my $files;
- while(<FILELIB>){
- my ($lib) = split(/\s+/, $_);
- my $i = 1;
- while(-e "reads/$base_name.$lib.file$i.fa"){
- $files->{"reads/$base_name.$lib.file1.fa"}++;
- $i++;
- }
- }
- close FILELIB;
- my $unpaired = "reads/$base_name.singlereads.fasta";
- $files->{$unpaired}++ if(-e $unpaired);
- foreach my $f(keys %$files){ $fnames.="$f,";}
- chop $fnames;
-
- #build bowtie index of contigs and map reads to the index
- my $bowtieout = $base_name . ".$library.bowtieIndex";
- my $bowbuildpath = "$Bin"."/bowtie/bowtie-build";
- my $bowtiepath = "$Bin"."/bowtie/bowtie";
- $bowtiepath =~ s/ /\\ /g;
- $bowbuildpath =~ s/ /\\ /g;
- die "Contig file ($contigFile) not found. Exiting...\n" if(!(-e $contigFile));
- &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
- system("$bowbuildpath $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
- &printMessage("\n=>".getDate().": Mapping reads to Bowtie index\n");
- my $procline = "$bowtiepath -p $threads -v $gaps bowtieoutput/$bowtieout -f $fnames --quiet -S |";
-
- #map reads with bowtie and obtain unmapped reads. Store the unmapped reads into a hash and use them for contig extension
- open(IN, "$procline") || die "Can't open bowtie output -- fatal\n";
- my ($counter, $step) = (0, 100000);
- my ($orig, $rc, $subrv,$subnor, $orig_mer);
- while(<IN>){
- my @t = split(/\t/);
- next if ($t[2] ne '*');
- if(++$counter == $step){
- CounterPrint($counter);
- $step = $step + 100000;
- }
- $orig_mer = length($t[9]);
- $rc=reverseComplement($t[9]);
- $MAX=$orig_mer if ($orig_mer > $MAX);
- $bin->{substr($t[9], 0, 10)}{$t[9]}++;
- $bin->{substr($rc, 0, 10)}{$rc}++;
- }
-
- print SUMFILE "CONTIG EXTENSION:\n".$seplines;
- print SUMFILE "\tNumber of unmapped reads used for contig extension = $counter\n";
- CounterPrint((" " x length($counter)));
-}
-
-###FUNCTION TO REVERSE COMPLEMENT A SEQUENCE
-sub reverseComplement{
- $_ = shift;
- tr/ATGC/TACG/;
- return (reverse());
-}
-
-###PRINTS A COUNTER ON THE SCREEN AND OVERWRITES PREVIOUS LINE
-sub CounterPrint{
- my $countingMessager = shift;
- print "\r$countingMessager";
- $|++;
-}
-
-###FUNCTION TO PRINT MESSAGES TO THE SCREEN AND TO THE LOG FILE
-sub printMessage{
- my $message = shift;
- print $message;
- print LOG $message;
-}
-
-###FUNCTION TO GET THE CURRENT DATE
-sub getDate{
- my $date = scalar(localtime);
- return $date;
-}
-
-###FLUSHES THE SUMMARY AND LOG FILE
-sub FlushFiles{
- select((select(SUMFILE), $| = 1)[0]);
- select((select(LOG), $| = 1)[0]);
- $|++;
-}
-
-sub checkStatus{
- &printMessage(("*" x 50)."\n\nProcess failed on ".getDate()."\n\n\n"), exit if(!(-d "process_OK"));
- rmtree(["process_OK", 'blurfl/quux']);
-}
-
-#########END ExtendOrFormatContigs.pl
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/sspace/bin/PairingAndScaffolding.pl b/external/gatb-minia-pipeline/sspace/bin/PairingAndScaffolding.pl
deleted file mode 100755
index 902ee5b784e5bc0e5666d18fc7b5e3aa848ef86c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/bin/PairingAndScaffolding.pl
+++ /dev/null
@@ -1,995 +0,0 @@
- ###################################################
- #Marten Boetzer 14-07-2011 #
- #SSPACE perl subscript PairingAndScaffolding.pl #
- #This script; #
- # -reads the contig sequences in a hash #
- # -stores Bowtie output in a hash #
- # -pairs the contigs #
- # -generates scaffolds #
- ###################################################
-
-
- #THIS VERSION OF SCAFFOLDING FIRST ORDERS THE CONTIGS BASED ON THE NUMBER OF INGOING LINKS AND STARTS AT LOWEST LEVEL. AFTER ALL THESE CONTIGS ARE SCAFFOLDED, INGOING LINKS ARE RECALCULATED OF REMAINING CONTIGS, ITERATIVELY.
- #ALSO, EACH CONTIG IS REPRESENTED ONCE IN THE SCAFFOLDS.
- #METHOD OF SCAFFOLDING IS; IF MORE THAN ONE LINK, CHECK IF THOSE LINKS HAVE CONNECTION WITH EACH OTHER. IF SO, COMBINE THEM IN THE SCAFFOLD. IF NOT, ESTIMATE RATIO AND ONLY ALLOW EXTENSION OF SCAFFOLD IF IT'S BELOW THE RATIO THRESHOLD GIVEN BY THE USER.
- #FUTURE: INCLUDE NUMBER OF REPEATS THAT ARE POSSIBLY PRESENT
- use strict;
- use Storable;
- use File::Path;
- use File::Basename;
- my ($Bin, $gaps);
- my $seplines = ("-" x 60)."\n";
- my $Bin = $ARGV[0];
- my $gaps = $ARGV[1];
- my $contig = $ARGV[2];
- my $base_name = $ARGV[3];
- my $issues = $ARGV[4];
- my $distribution = $ARGV[5];
- my $verbose = $ARGV[6];
- my $library = $ARGV[7];
- my $insert_size = $ARGV[8];
- my $min_allowed = $ARGV[9];
- my $scaffold = $ARGV[10];
- my $min_links = $ARGV[11];
- my $max_link_ratio = $ARGV[12];
- my $ori = $ARGV[13];
- my $threads = $ARGV[14];
- my $tab = $ARGV[15];
- my $tabfile = $ARGV[16];
- my $origctg = $ARGV[17];
- my $prev_evidence = $ARGV[18];
-
- my ($low_iz, $up_iz) = ($insert_size + $min_allowed, $insert_size - $min_allowed);
- my $bowtiefile = "bowtieoutput/" . $base_name . ".$library.mapped";
- my $log = $base_name . ".logfile.txt";
- my $summaryfile = $base_name.".summaryfile.txt";
-
- my ($total_for_median, $step,$ct_illogical, $ct_ok_contig, $ct_ok_pairs, $ct_problem_pairs, $ct_iz_issues, $ct_single, $ct_both, $counter)= (0,100000,0,0,0,0,0,0,0,0 );
- my ($pair,$err,$track_insert, $tigOnScafHash, $tigHash);
- my $pair_found = 0;
-
- open (LOG, ">>$log") || die "Can't write to $log -- fatal\n";
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- open(PET, ">$issues") || die "Can't open $issues for writing -- fatal\n";
-#-------------------------------------------------READ CONTIGS INTO HASH AND STORE THEIR LENGTH. NEXT; PAIR THE CONTIGS
- if($tab){
- parseEvidenceFile($prev_evidence) if($prev_evidence ne '');
- &updateContigs($origctg);
- }
- my ($contigstored, $tig_length) = &readFileContigHash($contig);
- if(!$tab){
- my $up_iz = ($insert_size - $min_allowed);
- my $newcontig = processContig($contig, $up_iz) ;
-
- my $fname = "reads/$base_name.$library.file1.fa";
- if(-e $fname){
- my $fname2 = "reads/$base_name.$library.file2.fa";
- my $i = 2;
- while(-e $fname2){
- $fname = "$fname,$fname2";
- $i++;
- $fname2 = "reads/$base_name.$library.file$i.fa";
- }
- }
- mapReadsWithBowtie($newcontig, $fname,$gaps, $threads);
- }else{
- parseTabFile($tigHash);
- }
- &printResultsPairing();
-
-#-------------------------------------------------BUILDING SCAFFOLDS
- &buildScaffolds($pair, $tig_length, $verbose, $scaffold, $library);
- ($pair, $tig_length) = ('',''); undef $pair; undef $tig_length;
-
- close SUMFILE;
- close LOG;
- mkpath('process_OK');
-
-#-------------------------------------------------
-
-###FUNCTION TO PARSE THE TAB FILE
-sub parseTabFile{
- my ($tigHash) = @_;
- open(TAB, "$tabfile") || die "Can't open $tabfile for reading -- fatal\n";
- my $lower = ($up_iz+200);
- my $step = 1000000;
- &printMessage("\n=>".getDate().": Parsing Tab file\n");
- while(<TAB>){
- chomp;
- if(++$ct_both == $step){
- CounterPrint($ct_both);
- $step = $step + 1000000;
- }
- my ($tig1,$start1,$end1,$tig2,$start2,$end2) = split(/\t/);
-
- #check if the contig in the tab file is also present in the inserted contig fasta file
- if(!defined($tigHash->{$tig1})){
- die "\nERROR: could not find an header containing $tig1 at line number $ct_both. Exit...\n";
- }
- if(!defined($tigHash->{$tig2})){
- die "ERROR: could not find an header containing $tig2 at line number $ct_both. Exit...\n";
- }
- my $ctg1 = $tigHash->{$tig1};
- my $ctg2 = $tigHash->{$tig2};
- my ($track1, $track2) = ("","");
-
- #if multiple libraries were used, update the contig positions in the TAB File by finding its position in the scaffolds
- if($prev_evidence ne ''){
- $start1 = $start1 + $tigOnScafHash->{$ctg1}{'begin'};
- $end1 = $end1 + $tigOnScafHash->{$ctg1}{'begin'};
- $start2 = $start2 + $tigOnScafHash->{$ctg2}{'begin'};
- $end2 = $end2 + $tigOnScafHash->{$ctg2}{'begin'};
- if($tigOnScafHash->{$ctg1}{'direction'} eq "r"){
- my $tmp_start = ($tigOnScafHash->{$ctg1}{'end'}+$tigOnScafHash->{$ctg1}{'begin'}) - $start1;
- my $tmp_end = ($tigOnScafHash->{$ctg1}{'end'}+$tigOnScafHash->{$ctg1}{'begin'}) - $end1;
- $start1 = $tmp_start;
- $end1 = $tmp_end;
- }
- if($tigOnScafHash->{$ctg2}{'direction'} eq "r"){
- my $tmp_start = ($tigOnScafHash->{$ctg2}{'end'}+$tigOnScafHash->{$ctg2}{'begin'}) - $start2;
- my $tmp_end = ($tigOnScafHash->{$ctg2}{'end'}+$tigOnScafHash->{$ctg2}{'begin'}) - $end2;
- $start2 = $tmp_start;
- $end2 = $tmp_end;
- }
-
- $ctg1 = $tigOnScafHash->{$ctg1}{'scaf'};
- $ctg2 = $tigOnScafHash->{$ctg2}{'scaf'};
- if($start1 < $lower || ($end1 > ($tig_length->{$ctg1}-$lower))){
- $track1 = "$ctg1"."|$start1"."|$end1";
- }
- if($start2 < $lower || ($end2 > ($tig_length->{$ctg2}-$lower))){
- $track2 = "$ctg2"."|$start2"."|$end2";
- }
- }else{ #if it is the first library, just use the positions in the TAB file
- if($start1 < $lower || ($end1 > ($tig_length->{$ctg1}-$lower))){
- $track1 = "$ctg1"."|$start1"."|$end1";
- }
- if($start2 < $lower || ($end2 > ($tig_length->{$ctg2}-$lower))){
- $track2 = "$ctg2"."|$start2"."|$end2";
- }
-
- }
- #pair the contigs based on the information provided in the TAB file
- pairContigs($track1, $track2, "seq$ct_both.1", "seq$ct_both.2") if($track1 ne "" && $track2 ne "");
- }
- CounterPrint(" ");
-}
-
-###FUNCTION TO STORE ONLY THE EDGES OF THE CONTIGS. ONLY READS ARE MAPPED TO THESE EDGES, SAVING TIME FOR BUILDING THE INDEX WITH BOWTIE, AND MAPPING THE READS TO THE CONTIGS
-sub processContig{
- my ($contigfile, $max_dist) = @_;
-
- my $lower = ($max_dist+200);
-
- open(IN,$contigfile) || die "can't read $contigfile -- fatal\n";
- my $contigfilesub = "tmp.$base_name/subset_contigs.fasta";
- open(OUT,">$contigfilesub") || die "can't write to $contigfilesub -- fatal\n";
- my ($seq, $counter) = ('', 0);
- while(<IN>){
- chomp;
- my $line = $_;
- $seq.= uc($line) if(eof(IN));
- if (/\>(\S+)/ || eof(IN)){
- if($seq ne ''){
- $counter++;
- if(length($seq) > (($lower * 2)+100)){
- my $upper = (length($seq) - ($lower));
- my $first = substr($seq, 0, $lower);
- my $second = substr($seq, $upper);
- my $newseq = $first."NNN".$second;
- print OUT ">$counter\n$newseq\n";
- }
- else{
- print OUT ">$counter\n$seq\n";
- }
- }
- $seq='';
- }else{
- $seq.=uc($line);
- }
- }
- close IN;
- close OUT;
- return $contigfilesub;
-}
-
-###FUNCTION TO PARSE THE EVIDENCE FILE, ONLY USED IF TAB FILE IS INSERTED
-#Function determines the position of the contigs on the scaffolds, information is used to update the contigs of the TAB file
-sub parseEvidenceFile{
- my ($file) = @_;
- my $track_tigs;
- open(IN,$file) || die "Can't open $file -- fatal\n";
- my $scaf = 0;
- my $totalsize= 0;
- while(<IN>){
- chomp;
- if(/^>/){
- $scaf++;
- $totalsize=0;
- }else{
- my ($tig, $size, $links, $gap, $merge) = split(/\|/,$_);
- if($tig ne ""){
- my ($direction, $tig2) = split(/_tig/,$tig);
- $tigOnScafHash->{$tig2}{'begin'} = $totalsize;
-
- my (undef, $size2) = split(/size/,$size);
- my $end = $totalsize + $size2;
- if($merge ne ""){
- my (undef, $merge2) = split(/merged/,$merge);
- $totalsize = $totalsize + ($size2 - $merge2);
- }elsif($gap ne ""){
- my (undef, $gap2) = split(/gaps/,$gap);
- $gap2 = 1 if($gap2 < 0);
- $totalsize = $totalsize + $size2 + $gap2;
- }else{
- $totalsize = $totalsize + $size2;
- }
- $tigOnScafHash->{$tig2}{'scaf'} = $scaf;
- $tigOnScafHash->{$tig2}{'end'} = $totalsize;
- $tigOnScafHash->{$tig2}{'direction'} = $direction;
- }
- }
- }
-}
-
-###FUNCTION TO UPDATE THE ORIGINAL CONTIG FILE INSERTED BY THE USER, SO MULTIPLE TAB FILES OF SEVERAL LIBRARIES CAN BE INSERTED
-sub updateContigs{
- my ($file, $update) = @_;
-
- &printMessage("\n=>".getDate().": Updating contig file\n");
-
- my ($countContig, $seq, $prevhead) = (0, "", '');
- open(IN,$file) || die "Can't open $file -- fatal\n";
- while(<IN>){
- my $line = $_;
- chomp $line;
- $seq.= $line if(eof(IN));
- if (/\>(\S+)/ || eof(IN)){
- my $head=$1;
- if($prevhead ne ''){
- ++$countContig;
- $tigHash->{$prevhead} = $countContig;
- }
- $prevhead = $head;
- $seq='';
- }else{
- $seq.=$line;
- }
- }
- CounterPrint(" ");
- &FlushFiles();
-}
-
-#READ THE CONTIG TO A HASH AND STORE THIS HASH
-sub readFileContigHash{
- my ($file) = @_;
-
- &printMessage("\n=>".getDate().": Reading contig file\n");
-
- my ($contigs, $tig_length);
- my ($countContig, $seq, $prevhead, $step) = (0, "", '', 1000);
- open(IN,$file) || die "Can't open $file -- fatal\n";
- while(<IN>){
- my $line = $_;
- chomp $line;
- $seq.= $line if(eof(IN));
- if (/\>(\S+)/ || eof(IN)){
- my $head=$1;
- if($prevhead ne ''){
- if(++$countContig == $step){
- CounterPrint($countContig);
- $step = $step + 100000;
- }
- $tig_length->{$countContig} = length($seq);
- $contigs->{$countContig}{'name'} = $prevhead;
- $contigs->{$countContig}{'seq'} = $seq;
- }
- $prevhead = $head;
- $seq='';
- }else{
- $seq.=$line;
- }
- }
- CounterPrint(" ");
- &FlushFiles();
- my $contigstore = "tmp.$base_name/contigs.stored";
- store \%$contigs, "$contigstore";
- undef $contigs;
- return ($contigstore, $tig_length);
-}
-
-###FUNCTION THAT FILTERS OUT THE REPEATS BY FINDING CONTIGS THAT HAVE MULTIPLE LINKS WITH OTHER CONTIGS
-sub determineRepeats{
- my ($tig_length, $repeathash) = @_;
- my $removeHash;
- #go through each contig
- foreach my $tig (sort {$tig_length->{$b}<=>$tig_length->{$a}} keys %$tig_length){
- for(my $i = 0; $i < 2; $i++){
- my $dtig = "r" . $tig;
- $dtig = "f" . $tig if($i);
- my $list = $pair->{$dtig}; #get contig pairs from $tig
- my ($seen_it, $matchhash);
- my $ct=0;
- #Go through each contig pair and get the number of links and gapsize
- foreach my $match (sort {$list->{$b}{'links'}<=>$list->{$a}{'links'}} keys %$list){
- my $matchnum = $1 if($match=~/[fr](\w+)/);
- print TMP "$dtig has $list->{$match}{'links'} links with $match and gap of ".int($list->{$match}{'gaps'}/$list->{$match}{'links'})." bases\n" if($list->{$match}{'links'} >= $min_links);
- if($list->{$match}{'links'} >= $min_links && !defined $seen_it->{$matchnum} && $ct < 2){
- $ct++;
- $matchhash->{$match}{'links'} = $list->{$match}{'links'};
- $matchhash->{$match}{'gaps'} = $list->{$match}{'gaps'};
- $matchhash->{$match}{'ratio'} = $list->{$match}{'gaps'}/$list->{$match}{'links'};
- $seen_it->{$matchnum}++;
- }
- }
- my @arraymatch;
- foreach my $ratiosort (sort {$matchhash->{$a}{'ratio'}<=>$matchhash->{$b}{'ratio'}} keys %$matchhash){
- push @arraymatch, $ratiosort;
- }
- my $repeat = 1;
- my $used;
- my $nummatch = $#arraymatch;
- #only determine if contig is a repeat if it has more than 1 link with other contigs
- if($nummatch > 0){
- my $listmatch = $pair->{$arraymatch[0]};
- #if the top two pairs of $tig have link with each other, establish their link so they are combined in scaffolding stage
- if($listmatch->{$arraymatch[1]}{'links'} >= $min_links){
- $pair = establishLink($dtig, $arraymatch[0], $pair);
- $pair = establishLink($arraymatch[0], $arraymatch[1], $pair);
- }else{ #otherwise, the contig has multiple links and is likely a repeat
- my @linkmatch;
- foreach my $linksort (sort {$matchhash->{$b}{'links'}<=>$matchhash->{$a}{'links'}} keys %$matchhash){
- push @linkmatch, $linksort;
- }
- my ($ratio2, $first, $second) = (0,"","");
-
- #check for two ratio's between the two best contig pairs. One is a ratio of the links, other is the number of links per searchspace.
- #If either one of the two ratio's is above the user-defined (-a) ratio, the original contig is treated as a repeat
-
- #estimate the ratio of the links of the two best contig pairs (ratio 1)
- my $link1 = $matchhash->{$linkmatch[1]}{'links'};
- my $link2 = $matchhash->{$linkmatch[0]}{'links'};
- my $ratio1 = $link1 / $link2; ## relative ratio of the two most abundant contig pairs
- $ratio1 = sprintf("%.2f", $ratio1);
- $first = $linkmatch[0];
- #estimate the number of links per gap for the two best contig pairs and divide them (ratio 2)
- my $gapPerSpace1 = estimateLinksPerGap($matchhash, $linkmatch[0], $insert_size, $tig_length);
- my $gapPerSpace2 = estimateLinksPerGap($matchhash, $linkmatch[1], $insert_size, $tig_length);
- if($gapPerSpace1 > $gapPerSpace2){
- $second = $linkmatch[0];
- $ratio2 = $gapPerSpace2/$gapPerSpace1;
- }else{
- $second = $linkmatch[1];
- $ratio2 = $gapPerSpace1/$gapPerSpace2;
- }
- my $revdtig = $dtig;
- $revdtig =~ tr/fr/rf/;
- #if one of the two ratio's is above the user-defined (-a) option, contig is a repeat and all links with this contig are removed
- if($ratio2 >= $max_link_ratio || $ratio1 >= $max_link_ratio || $first ne $second){
- foreach my $linksort (sort {$list->{$b}{'links'}<=>$list->{$a}{'links'}} keys %$list){
- my $num = $1 if($linksort=~/[fr](\w+)/);
- $removeHash->{$dtig}{$linksort}++;
- my $revlinksort = $linksort;
- $revlinksort =~ tr/fr/rf/;
- $removeHash->{$revdtig}{$revlinksort}++;
- }
- }
- else{ #otherwise, establish the link between the most likely contig pair
- foreach my $linksort (sort {$list->{$b}{'links'}<=>$list->{$a}{'links'}} keys %$list){
- if($linksort ne $first){
- my $num = $1 if($linksort=~/[fr](\w+)/);
- my $revlinksort = $linksort;
- $revlinksort =~ tr/fr/rf/;
- $removeHash->{$revdtig}{$revlinksort}++;
- $removeHash->{$dtig}{$linksort}++;
- }
- }
- }
- }
- }
- }
- }
- return $removeHash;
-}
-
-###FUNCTION TO ESTABLISH A LINK BETWEEN CONTIGS SO THESE CONTIGS ARE PAIRED DURING SCAFFOLDING
-sub establishLink{
- my ($tig1, $tig2, $pair) = @_;
- my $list = $pair->{$tig1};
- my $revtig1 = $tig1;
- $revtig1 =~ tr/fr/rf/;
- my $revtig2 = $tig2;
- $revtig2 =~ tr/fr/rf/;
- foreach my $rep (keys %$list){
- if($rep ne $tig2 && $rep ne $revtig2){
- delete $pair->{$tig1}{$rep};
- $rep =~ tr/fr/rf/;
- delete $pair->{$rep}{$revtig1};
- }
- }
- my $list2 = $pair->{$revtig2};
- foreach my $rep2 (keys %$list2){
- if($rep2 ne $tig1 && $rep2 ne $revtig1){
- delete $pair->{$revtig2}{$rep2};
- $rep2 =~ tr/fr/rf/;
- delete $pair->{$rep2}{$tig2};
- }
- }
-
- return $pair;
-}
-
-###DETERMINE THE NUMBER OF LINKS PER GAP, BASED ON INSERT SIZE
-sub estimateLinksPerGap{
- my ($linkhash, $tig1, $insert_size, $length_hash) = @_;
- my $t1 = $1 if($tig1=~/[fr](\w+)/);
- my $space = 0;
- my $gap = int($linkhash->{$tig1}{'ratio'});
- $gap = 0 if($linkhash->{$tig1}{'ratio'} < 0);
- if(($length_hash->{$t1}+$gap) >= $insert_size){
- $space = int($insert_size - $gap);
- }else{
- $space =$length_hash->{$t1};
- }
- my $ratio = $linkhash->{$tig1}{'links'}/$space;
- return $ratio;
-}
-
-###FUNCTION TO BUILD THE SCAFFOLDS
-sub buildScaffolds{
- my ($pair, $tig_length, $verbose, $scaffold, $lib) = @_;
- &printMessage("\n=>".getDate().": Building scaffolds file\n");
-
- open (SC, ">$scaffold") || die "Can't write to $scaffold -- fatal\n";
- my ($sc_ct, $keyrep, $numrepeat) = (0,0,0);
- my ($repeathash, $seen_start);
-
- #determine the repeats and remove any link if contig is a repeat
- #if contig has multiple links, but one considered to be the 'best', establish this contig-pair by removing the links with other contigs
- open (TMP, ">intermediate_results/$base_name"."_$library.foundlinks") || die "Can't write to intermediate_results/$base_name"."_$library.foundlinks -- fatal\n";
- $repeathash = determineRepeats($tig_length, $repeathash);
- close TMP;
- open (REPEAT, ">intermediate_results/$base_name"."_$library.repeats") || die "Can't write to intermediate_results/$base_name"."_$library.repeats -- fatal\n";
- foreach my $rep (sort keys %$repeathash){
- my $tig = $1 if($rep=~/[fr](\w+)/);;
- my $ls = $repeathash->{$rep};
- my ($num_match,$repline) = (0,"");
- foreach my $rep2 (sort keys %$ls){
- if($pair->{$rep}{$rep2}{'links'} >= $min_links){
- $repline.="\twith $rep2 (links = $pair->{$rep}{$rep2}{'links'})\n";
- $num_match++;
- }
- delete $pair->{$rep}{$rep2};
- delete $pair->{$rep2}{$rep};
- }
- if($num_match > 1){
- $numrepeat++;
- print REPEAT "Contig $rep (size = $tig_length->{$tig}) has $num_match multiple links;\n";
- print REPEAT "$repline\n";
- }
- }
- close REPEAT;
- print SUMFILE "REPEATS: \n";
- print SUMFILE "\tNumber of repeated edges = $numrepeat\n$seplines\n";
-
- #go through each contig and find contig pairs left and right, forming scaffolds
- SEED:
- foreach my $tig (sort {$tig_length->{$b}<=>$tig_length->{$a}} keys %$tig_length){
- my $ftig = "f" . $tig;
- my $rtig = "r" . $tig;
-
- if(! defined $seen_start->{$tig}){##should prevent re-using a contig as seed if it's already been incorporated into a scaffold
- CounterPrint(++$sc_ct);
- my $chainleft = "";
- my $ori_chainright = $ftig . "Z" . $tig_length->{$tig};
- my $chainright = $ori_chainright;
- my $total = $tig_length->{$tig};
- ($total, $chainright, $seen_start) = &computeLayout("R", $chainright, $ftig, $pair, $tig_length, $total, $seen_start, $tig);
- ($total, $chainleft, $seen_start) = &computeLayout("L", $chainleft, $rtig, $pair, $tig_length, $total, $seen_start, $tig);
-
- delete $pair->{$ftig};
- delete $pair->{$rtig};
- delete $tig_length->{$tig};
- $seen_start->{$tig}++;
- my $scaffold = $chainleft . $chainright;
- print SC "scaffold" . $sc_ct . ",$total,$scaffold\n";
- }
- }
- CounterPrint(" ");
- close SC;
- &FlushFiles();
-}
-
-# links contigs together into a chain - must satisfy user-defined criterions (-k -a)
-sub computeLayout{
- my ($ext, $chain, $tig, $pair, $tig_length, $total, $seen_start, $orig_tig_number) = @_;
- my $orig_tig = $tig;
- my $extension = 1;
- EXTENSION:
- while($extension){
- my $tnum = $1 if($tig=~/[fr](\w+)/);
- my $tnumf = "f" . $tnum;
- my $tnumr = "r" . $tnum;
- my $ratio = 0.00;
- if(!defined $seen_start->{$tnum}){ #if already seen in scaffold, do not use it again
- $seen_start->{$tnum}++ if($tnumf ne $orig_tig);
- my $list = $pair->{$tig};
- my $matchhash;
- my ($match1,$link1,$gaps1,$match2,$link2,$gaps2,$cntloop, $countmatches)=("",0,0,"",0,0,0,0);
- my $ct=0;
- LINK:
- foreach my $match (sort {$list->{$b}{'links'}<=>$list->{$a}{'links'}} keys %$list){
- my $matchnum = $1 if($match=~/[fr](\w+)/);
- if($list->{$match}{'links'} >= $min_links && !defined $seen_start->{$matchnum} && $matchnum ne $orig_tig_number && $ct < 2){
- $ct++;
- $matchhash->{$match}{'links'} = $list->{$match}{'links'};
- $matchhash->{$match}{'gaps'} = $list->{$match}{'gaps'};
- $matchhash->{$match}{'ratio'} = $list->{$match}{'gaps'}/$list->{$match}{'links'};
- $countmatches++;
- }else{
- last LINK;
- }
- }
- my $foundlinks = 0;
- if($countmatches > 1){
- my @arraymatch;
- foreach my $ratiosort (sort {$matchhash->{$a}{'ratio'}<=>$matchhash->{$b}{'ratio'}} keys %$matchhash){
- push @arraymatch, $ratiosort;
- }
- my $nummatch = $#arraymatch;
- for(my $i=0; $i <= $nummatch && $foundlinks < 1; $i++){
- my $listmatch = $pair->{$arraymatch[$i]};
- for(my $j=$i+1; $j <= $nummatch && $foundlinks < 1; $j++){
- my $linkmatch = $listmatch->{$arraymatch[$j]}{'links'};
- $foundlinks = 1 if(!($linkmatch >= $min_links));
- }
- }
- my $tignum = $1 if($arraymatch[$nummatch]=~/[fr](\w+)/);
- $countmatches=0 if(!$foundlinks && defined $seen_start->{$tignum});
- }if($foundlinks && $countmatches > 1){
- my @linkmatch;
- foreach my $linksort (sort {$matchhash->{$b}{'links'}<=>$matchhash->{$a}{'links'}} keys %$matchhash){
- push @linkmatch, $linksort;
- }
- my $linkhash;
- my $link1 = $matchhash->{$linkmatch[1]}{'links'};
- my $link2 = $matchhash->{$linkmatch[0]}{'links'};
- my $ratio = $link1 / $link2; ## relative ratio of the two most abundant contig pairs
- $ratio = sprintf("%.2f", $ratio);
-
- if($ratio <= $max_link_ratio){
- foreach my $mat (keys %$matchhash){
- delete $matchhash->{$mat} if($mat ne $linkmatch[0]);
- }
- $foundlinks = 0;
- $countmatches = 1;
- }
- }
- if((!$foundlinks) && $countmatches > 0){
- my $nummatch =0;
- my @chainlist;
- my @tiglist;
- foreach my $incl_matches (sort {$matchhash->{$a}{'ratio'}<=>$matchhash->{$b}{'ratio'}} keys %$matchhash){
- if($tig ne $incl_matches){
- $nummatch++;
- my $listmatch = $pair->{$tig};
- my $tempnum = $1 if($incl_matches =~ /[fr](\w+)/);
- my $link2 = $listmatch->{$incl_matches}{'links'};
- my $mean2 = $listmatch->{$incl_matches}{'gaps'}/$link2;
-
- $seen_start->{$tempnum}++if($nummatch < $countmatches);
-
- ($chain, $total, $tig) = &getChain($chain, $ext, $link2, $mean2, $incl_matches, $tempnum, $ratio, $tig_length, $total);
- delete $tig_length->{$tempnum};
- }
- }
- $extension = 1;
-
- }else{
- $extension = 0;
- last EXTENSION;
- }
- }else{
- $extension = 0;
- last EXTENSION;
- }
- }
- return $total, $chain, $seen_start;
-}
-
-###function to combine contigs into a scaffold
-sub getChain{
- my ($chain, $ext, $link, $mean, $match, $tempnum, $ratio, $tig_length, $total) = @_;
- my $tig = $match;
- if($ext eq "R"){
- $chain .= "k" . $link . "a" . $ratio . "m" . int($mean) . "_" . $match . "z" . $tig_length->{$tempnum};
- }else{
- my $temp_match = "";
- if($match =~ /^r(\d+)/){$temp_match = "f" . $1;}else{$temp_match = "r". $1;}
- $chain = $temp_match . "z" . $tig_length->{$tempnum} . "k" . $link . "a" . $ratio . "m" . int($mean) . "_" . $chain;
- }
-
- $total += $tig_length->{$tempnum};
- return ($chain, $total, $tig);
-}
-
-
-###GET THE DISTANCE BETWEEN TWO PAIRED READS
-sub getDistance{
-
- my ($insert_size, $length_i, $start_i, $start_j) = @_;
-
- # L ------ --------- R
- # i -> <- j
- # .... ...... insert_span
- # ============ insert_size
-
- my $insert_span = ($length_i - $start_i) + $start_j;
- my $gap_or_overlap = $insert_size - $insert_span;
-
- return $gap_or_overlap;
-}
-
-###Pair contigs based on mapping of two reads
-sub pairContigs{
- my ($trackA, $trackB, $read_a, $read_b) = @_;
- my ($tig_a, $A_start, $A_end) = split(/\|/, $trackA);
- my ($tig_b, $B_start, $B_end) = split(/\|/, $trackB);
- my ($ori_1,$ori_2) = split(//, $ori);
- if($ori_1 eq "R"){
- my ($tmp_A_start, $tmp_A_end) = ($A_start, $A_end);
- ($A_start, $A_end) = ($tmp_A_end, $tmp_A_start);
- }
- if($ori_2 eq "F"){
- my ($tmp_B_start,$tmp_B_end) = ($B_start,$B_end);
- ($B_start,$B_end) = ($tmp_B_end,$tmp_B_start);
- }
- my $ftig_a = "f" . $tig_a;
- my $ftig_b = "f" . $tig_b;
- my $rtig_a = "r" . $tig_a;
- my $rtig_b = "r" . $tig_b;
- my $A_length = $tig_length->{$tig_a};
- my $B_length = $tig_length->{$tig_b};
- if (($tig_a != $tig_b) || ($tig_a ne $tig_b)){####paired reads located on <> contigs
- ####Determine most likely possibility
- if ($A_start < $A_end){
- if ($B_end < $B_start){####-> <- ::: A-> <-B / rB -> <- rA
- my $d = &getDistance($insert_size, $A_length, $A_start, $B_start);
- print "A-> <-B WITH $tig_a -> <- $tig_b GAP $d A=$A_length ($A_start-$A_end) B=$B_length ($B_start-$B_end) Alen, Astart,Bstart\n" if($verbose);
- if($d >= $min_allowed){
- $pair->{$ftig_a}{$ftig_b}{'links'}++;
- $pair->{$ftig_a}{$ftig_b}{'gaps'} += $d;
- $pair->{$rtig_b}{$rtig_a}{'links'}++;
- $pair->{$rtig_b}{$rtig_a}{'gaps'} += $d;
- $ct_ok_pairs++;
- }else{
- my $err_pair = $ftig_a . "-". $ftig_b;
- $err->{$err_pair}{'links'}++;
- $err->{$err_pair}{'gaps'} += $d;
- $ct_problem_pairs++;
- print PET "Pairs unsatisfied in distance within a contig pair. A-> <-B WITH tig#$tig_a -> $d <- tig#$tig_b, A=$A_length nt (start:$A_start, end:$A_end) B=$B_length nt (start:$B_start, end:$B_end) CALCULATED DISTANCE APART: $d < $min_allowed\n";
- }
- }else{#### -> -> ::: A-> <-rB / B-> <-rA
- my $rB_start = $B_length - $B_start;
- my $d = &getDistance($insert_size, $A_length, $A_start, $rB_start);
- print "A-> <-rB WITH $tig_a -> <- r.$tig_b GAP $d A=$A_length ($A_start-$A_end) B=$B_length ($B_start-$B_end) Alen,Astart,rBstart\n"if($verbose);
- if($d >= $min_allowed){
- $pair->{$ftig_a}{$rtig_b}{'links'}++;
- $pair->{$ftig_a}{$rtig_b}{'gaps'} += $d;
- $pair->{$ftig_b}{$rtig_a}{'links'}++;
- $pair->{$ftig_b}{$rtig_a}{'gaps'} += $d;
- $ct_ok_pairs++;
- }else{
- my $err_pair = $ftig_a . "-". $rtig_b;
- $err->{$err_pair}{'links'}++;
- $err->{$err_pair}{'gaps'} += $d;
- $ct_problem_pairs++;
- print PET "Pairs unsatisfied in distance within a contig pair. A-> <-rB WITH tig#$tig_a -> $d <- tig#r.$tig_b, A=$A_length nt (start:$A_start, end:$A_end) B=$B_length nt (start:$B_start, end:$B_end) CALCULATED DISTANCE APART: $d < $min_allowed\n";
- }
- }
- }else{
- if ($B_end > $B_start){####<- -> ::: B-> <-A / rA -> <- rB
- my $d = &getDistance($insert_size, $B_length, $B_start, $A_start);
- print "B-> <-A WITH $tig_b -> <- $tig_a GAP $d A=$A_length ($A_start-$A_end) B=$B_length ($B_start-$B_end) Blen,Bstart,Astart\n" if($verbose);
- if($d >= $min_allowed){
- $pair->{$ftig_b}{$ftig_a}{'links'}++;
- $pair->{$ftig_b}{$ftig_a}{'gaps'} += $d;
- $pair->{$rtig_a}{$rtig_b}{'links'}++;
- $pair->{$rtig_a}{$rtig_b}{'gaps'} += $d;
- $ct_ok_pairs++;
- }else{
- my $err_pair = $ftig_b . "-". $ftig_a;
- $err->{$err_pair}{'links'}++;
- $err->{$err_pair}{'gaps'} += $d;
- $ct_problem_pairs++;
- print PET "Pairs unsatisfied in distance within a contig pair. B-> <-A WITH tig#$tig_b -> $d <- tig#$tig_a, B=$B_length nt (start:$B_start, end:$B_end) A=$A_length nt (start:$A_start, end:$A_end) CALCULATED DISTANCE APART: $d < $min_allowed\n";
- }
- }else{ ####<- <- ::: rB-> <-A / rA-> <-B
- my $rB_start = $B_length - $B_start;
- my $d = &getDistance($insert_size, $B_length, $rB_start, $A_start);
- print "rB-> <-A WITH r.$tig_b -> <- $tig_a GAP $d A=$A_length ($A_start-$A_end) B=$B_length ($B_start-$B_end) Blen,rBstart,Astart\n" if($verbose);
- if($d >= $min_allowed){
- $pair->{$rtig_b}{$ftig_a}{'links'}++;
- $pair->{$rtig_b}{$ftig_a}{'gaps'} += $d;
- $pair->{$rtig_a}{$ftig_b}{'links'}++;
- $pair->{$rtig_a}{$ftig_b}{'gaps'} += $d;
- $ct_ok_pairs++;
- }else{
- my $err_pair = $rtig_b . "-". $ftig_a;
- $err->{$err_pair}{'links'}++;
- $err->{$err_pair}{'gaps'} += $d;
- $ct_problem_pairs++;
- print PET "Pairs unsatisfied in distance within a contig pair. rB-> <-A WITH tig#r.$tig_b -> $d <- tig#$tig_a, B=$B_length nt (start:$B_start, end:$B_end) A=$A_length nt (start:$A_start, end:$A_end) CALCULATED DISTANCE APART: $d < $min_allowed\n";
- }
- }
- }
- }else{###Clone, paired reads located on the same contig -- could be used to investigate misassemblies
- print "Pair ($read_a and $read_b) located on same contig $tig_a ($A_length nt)\n" if ($verbose);
- my $pet_size = 0;
-
- if ($A_start > $B_start && ($B_start < $B_end) && ($A_start > $A_end)){ # B --> <-- A
- $total_for_median++;
- $pet_size = $A_start - $B_start;
- $track_insert->{$pet_size}++;
- if($pet_size >= $low_iz && $pet_size <= $up_iz){
- $ct_ok_contig++;
- }else{
- print PET "Pairs unsatisfied in distance within a contig. Pair ($read_a - $read_b) on contig $tig_a ($A_length nt) Astart:$A_start Aend:$A_end Bstart:$B_start Bend:$B_end CALCULATED DISTANCE APART: $pet_size\n";
- $ct_iz_issues++;
- }
- }elsif($B_start > $A_start && ($B_start > $B_end) && ($A_start < $A_end)){ # A --> <-- B
- $total_for_median++;
- $pet_size = $B_start - $A_start;
- $track_insert->{$pet_size}++;
- if($pet_size >= $low_iz && $pet_size <= $up_iz){
- $ct_ok_contig++;
- }else{
- print PET "Pairs unsatisfied in distance within a contig. Pair ($read_a - $read_b) on contig $tig_a ($A_length nt) Astart:$A_start Aend:$A_end Bstart:$B_start Bend:$B_end CALCULATED DISTANCE APART: $pet_size\n";
- $ct_iz_issues++;
- }
- }else{
- $ct_illogical++;
- print PET "Pairs unsatisfied in pairing logic within a contig. Pair ($read_a - $read_b) on contig $tig_a ($A_length nt) Astart:$A_start Aend:$A_end Bstart:$B_start Bend:$B_end\n";
- }
- }
-}
-
-###Print read pairing results to the summary file, including estimation of mean and median insert size
-sub printResultsPairing{
- print PET "------------- Putative issues with contig pairing - Summary ----------------\n";
- foreach my $err_pair (sort {$err->{$b}{'links'}<=>$err->{$a}{'links'}} keys %$err){
- my $mean_iz = 0;
- $mean_iz = $err->{$err_pair}{'gaps'} / $err->{$err_pair}{'links'} if ($err->{$err_pair}{'links'});
- print PET "Pair $err_pair has $err->{$err_pair}{'links'} links and mean distance = $mean_iz\n";
- }
- close PET;
-
- my $satisfied = $ct_ok_pairs + $ct_ok_contig;
- my $unsatisfied = $ct_problem_pairs + $ct_iz_issues + $ct_illogical;
- my $ct_both_reads = $ct_both * 2;
-
- #write distribution file
- open (CSV, ">$distribution") || die "Can't open $distribution for writing -- fatal";
- my ($total_is, $overal_is,$median_ins, $stdev,$record, $sumX,$sumX2) = (0,0,0,0,0,0,0);
- my $median_bin = int($total_for_median/2);
-
- foreach my $is (sort {$a<=>$b} keys %$track_insert){
- for(my $i=0;$i<$track_insert->{$is};$i++){
- $record++;
- $sumX += $is;
- $sumX2 += ($is * $is);
- $median_ins = $is if($record >= $median_bin && $median_ins == 0);
- }
- $overal_is += ($is * $track_insert->{$is});
- print CSV "$is,$track_insert->{$is}\n";
- }
- my ($mean_ins,$sigma) = (0,0);
- if($sumX > 0 && $record > 0){
- $mean_ins = int($sumX/$record);
- $sigma = sprintf("%.2f",sqrt($sumX2/$record - $mean_ins*$mean_ins));
- }
- close CSV;
-
- print SUMFILE "READ PAIRS STATS:\n";
- print SUMFILE "\tAssembled pairs: $ct_both ($ct_both_reads sequences)\n";
- print SUMFILE "\t\tSatisfied in distance/logic within contigs (i.e. -> <-, distance on target: $insert_size +/$min_allowed): $ct_ok_contig\n";
- print SUMFILE "\t\tUnsatisfied in distance within contigs (i.e. distance out-of-bounds): $ct_iz_issues\n";
- print SUMFILE "\t\tUnsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): $ct_illogical\n";
- print SUMFILE "\t\t---\n";
- print SUMFILE "\t\tSatisfied in distance/logic within a given contig pair (pre-scaffold): $ct_ok_pairs\n";
- print SUMFILE "\t\tUnsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): $ct_problem_pairs\n";
- print SUMFILE "\t\t---\n";
- print SUMFILE "\tTotal satisfied: $satisfied\tunsatisfied: $unsatisfied\n\n";
- print SUMFILE "\n\tEstimated insert size statistics (based on $total_for_median pairs): \n";
- print SUMFILE "\t\tMean insert size = $mean_ins\n";
- print SUMFILE "\t\tMedian insert size = $median_ins\n";
- # print SUMFILE "\t\tInsert size deviation = $sigma\n$seplines\n";
-
- &FlushFiles();
- return $pair;
-}
-
-###Function that maps the readfiles to the contigs
-sub mapReadsWithBowtie{
- my ($contigFile, $singlereads, $gaps, $threads) = @_;
- #building Index of contig and mapping reads to Index
- my $bowtieout = $base_name . ".$library.bowtieIndex";
- my $bowbuildpath = "$Bin"."/bowtie/bowtie-build";
- my $bowtiepath = "$Bin"."/bowtie/bowtie";
- $bowtiepath =~ s/ /\\ /g;
- $bowbuildpath =~ s/ /\\ /g;
-
- my @reads = split(/,/,$singlereads);
- foreach my $read (@reads){
- die "Single read file ($read) not found. Exiting...\n" if(!(-e $read));
- }
- my $procline = "$bowtiepath -p $threads -v $gaps -m 1 bowtieoutput/$bowtieout --suppress 6,7 -f $singlereads --quiet --refidx |";
- die "Contig file ($contigFile) not found. Exiting...\n" if(!(-e $contigFile));
- &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
- system("$bowbuildpath $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
-
- #Treat the output of Bowtie differently if multithreading is used or not
- readBowtieOneThread($procline) if($threads <= 1);
- readBowtieMultThread($procline) if($threads > 1);
-}
-
-###Parse output of Bowtie when only one thread of Bowtie is used
-sub readBowtieOneThread{
- my ($input) = @_;
- my $lower = ($up_iz+200);
- my $sub = ($lower * 2) + 3;
- my ($prevline, $line, $prevread, $counter, $step, $pair_found, $ct_pair) = ("","","",0, 1000000, 0, 0);
- my ($seq1, $seq2, $track1, $track2, $count);
-
- &printMessage("\n=>".getDate().": Mapping reads to contigs. Reading bowtie output and pairing contigs\n");
- open(IN, "$input") || die "Can't open bowtie output -- fatal\n";
- #go through mapping results
- while($line = <IN>){
- if(++$counter == $step){
- CounterPrint($counter);
- $step = $step + 1000000;
- }
- my ($read) = split(/\//,$line);
- if($prevread eq $read){
- $pair_found++;
- ($seq1, $track1) = StoreResults($prevline, $lower, $sub);
- ($seq2, $track2) = StoreResults($line, $lower, $sub);
- my $combined = "$seq1:$seq2";
- my $revcombined = reverseComplement($combined);
- if(!$count->{$combined} && !$count->{$revcombined}){
- $count->{$combined}++;
- pairContigs($track1, $track2, $seq1, $seq2);
- $ct_both++;
- }
- }
- $prevread = $read;
- $prevline = $line;
- }
- close IN;
- CounterPrint(" ");
- print SUMFILE "\nMAPPING READS TO CONTIGS:\n";
- print SUMFILE "$seplines\tNumber of single reads found on contigs = $counter\n";
- my $read_number_message = "\tNumber of pairs used for pairing contigs / total pairs = $ct_both / $pair_found\n";
- printf SUMFILE $read_number_message.$seplines."\n";
- &FlushFiles();
-}
-
-###Parse output of Bowtie when multiple threads of Bowtie are used
-sub readBowtieMultThread{
- my ($input) = @_;
- my $lower = ($up_iz+200);
- my $sub = ($lower * 2) + 3;
- my ($prevline, $line, $prevread, $counter, $step, $ct, $ctHash, $pair_found) = ("","","",0, 1000000,0,1,0);
- my ($seq1, $seq2, $track1, $track2, $count, $readHash);
-
- &printMessage("\n=>".getDate().": Mapping reads to contigs. Reading bowtie output and pairing contigs\n");
- open(IN,"$input") || die "Can't open bowtie output -- fatal\n";
- while ($line = <IN>) {
- if(++$ct >= ($ctHash*$step)){
- CounterPrint($ct);
- delete $readHash->{($ctHash-1)};
- $ctHash++;
- }
- my ($readname) = split(/\t/,$line);
- my ($read,$readnum) = split(/\//,$readname);
- if($readHash->{($ctHash-1)}{$read}){
- $pair_found++;
- if($readnum == 1){
- ($seq2, $track2) = StoreResults($readHash->{($ctHash-1)}{$read}, $lower, $sub);
- ($seq1, $track1) = StoreResults($line, $lower, $sub);
- }else{
- ($seq1, $track1) = StoreResults($readHash->{($ctHash-1)}{$read}, $lower, $sub);
- ($seq2, $track2) = StoreResults($line, $lower, $sub);
- }
- my $combined = "$seq1:$seq2";
- my $revcombined = reverseComplement($combined);
- if(!$count->{$combined} && !$count->{$revcombined}){
- $count->{$combined}++;
- pairContigs($track1, $track2, $seq1, $seq2);
- $ct_both++;
- }
- }elsif(defined $readHash->{$ctHash}{$read}){
- $pair_found++;
- if($readnum == 1){
- ($seq2, $track2) = StoreResults($readHash->{($ctHash)}{$read}, $lower, $sub);
- ($seq1, $track1) = StoreResults($line, $lower, $sub);
- }else{
- ($seq1, $track1) = StoreResults($readHash->{($ctHash)}{$read}, $lower, $sub);
- ($seq2, $track2) = StoreResults($line, $lower, $sub);
- }
- my $combined = "$seq1:$seq2";
- my $revcombined = reverseComplement($combined);
- if(!$count->{$combined} && !$count->{$revcombined}){
- $count->{$combined}++;
- pairContigs($track1, $track2, $seq1, $seq2);
- $ct_both++;
- }
- }
- $readHash->{$ctHash}{$read} = $line;
- }
- close IN;
- CounterPrint(" ");
- print SUMFILE "\nMAPPING READS TO CONTIGS:\n";
- print SUMFILE "$seplines\tNumber of single reads found on contigs = ". $ct."\n";
- my $read_number_message = "\tNumber of pairs used for pairing contigs / total pairs = $ct_both / $pair_found\n";
- printf SUMFILE $read_number_message.$seplines."\n";
- &FlushFiles();
-}
-
-sub StoreResults{
- my ($input, $lower, $sub) = @_;
- my ($read, $strand, $tig, $start, $seq) = split(/\t/,$input);
- my ($startval, $endval, $keyvalue) = (0,0,"");
- $tig++;
- if($start > $lower && $tig_length->{$tig} > (($lower * 2)+100)){
- my $minsub = $sub - $start;
- $start = ($tig_length->{$tig} - $minsub);
- }
- if($strand eq "+"){
- $startval = $start;
- $endval = $start + length($seq);
- }
- else{
- $startval = $start + length($seq);
- $endval = $start;
- $seq = reverseComplement($seq);
- }
- $keyvalue = "$tig"."|$startval"."|$endval";
- return $seq, $keyvalue;
-}
-
-###FUNCTION TO REVERSE COMPLEMENT A SEQUENCE
-sub reverseComplement{
- $_ = shift;
- tr/ATGC/TACG/;
- return (reverse());
-}
-
-###PRINTS A COUNTER ON THE SCREEN AND OVERWRITES PREVIOUS LINE
-sub CounterPrint{
- my $countingMessager = shift;
- print "\r$countingMessager";
- $|++;
-}
-
-###FUNCTION TO PRINT MESSAGES TO THE SCREEN AND TO THE LOG FILE
-sub printMessage{
- my $message = shift;
- print $message;
- print LOG $message;
-}
-
-###FUNCTION TO GET THE CURRENT DATE
-sub getDate{
- my $date = scalar(localtime);
- return $date;
-}
-
-###FLUSHES THE SUMMARY AND LOG FILE
-sub FlushFiles{
- select((select(SUMFILE), $| = 1)[0]);
- select((select(LOG), $| = 1)[0]);
- $|++;
-}
-
-#########END PairingAndScaffolding.pl
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/sspace/bin/readLibFiles.pl b/external/gatb-minia-pipeline/sspace/bin/readLibFiles.pl
deleted file mode 100755
index 130694fcb1da4c074eb79b9dc7417ad1d61c48e9..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/bin/readLibFiles.pl
+++ /dev/null
@@ -1,231 +0,0 @@
- #############################################################
- #Marten Boetzer 13-06-2011 #
- #SSPACE perl subscript readLibFiles.pl #
- #This script; #
- # -reads, converts and filters original input sequences #
- #############################################################
-
- use Storable;
- use File::Path;
- use File::Basename;
- use threads;
-
- my $seplines = ("-" x 60)."\n";
- my $maxlen = 0;
-
- my $libraryfile = $ARGV[0];
- my $base_name = $ARGV[1];
- my $extending = $ARGV[2];
- my $unpaired_file = $ARGV[3];
- my $min_overlap = $ARGV[4];
- my $thread = $ARGV[5];
- my $log = $base_name . ".logfile.txt";
- my $summaryfile = $base_name.".summaryfile.txt";
-
- open (SUMFILE, ">>$summaryfile") || die "Can't open $summaryfile -- fatal\n";
- open (LOG, ">>$log") || die "Can't write to $log -- fatal\n";
-
- my $filenameOutFilt = "filtered.readpairs.fasta";
- my $filenameOutExt = $base_name . ".singlereads.fasta";
-
-#-------------------------------------------------READ UNPAIRED FILE CONTAINING SINGLE READS
- &readUnpairedFile($unpaired_file) if ($unpaired_file);
-#-------------------------------------------------LOOP THROUGH EACH LIBRARY IN LIBRARYFILE AND STORE AND FILTER READS
- open(FILELIB, "< $libraryfile");
-
- my ($library, $fileA, $fileB, $insert_size, $insert_stdev, $reverse, $libResHash);
- my ($prevlibrary, $ctlib) = ("",0);
- &printMessage("\n=>".getDate().": Reading, filtering and converting input sequences of library file initiated\n");
-
- while(<FILELIB>){
- chomp;
- ($library, $fileA, $fileB, $insert_size, $insert_stdev, $reverse) = split(/\s+/, $_);
-
- next if($library eq "");
- $ctlib=0 if($library ne $prevlibrary && $prevlibrary ne "");
- $ctlib++;
-
- my ($fileBaseName1, $dirName1, $fileExtension1) = fileparse($fileA);
- my ($fileBaseName2, $dirName2, $fileExtension2) = fileparse($fileB);
-
- my $fname = "reads/$base_name.$library.filtered.readpairs.singles.fasta";
- my ($counter2, $Ncount2);
- #Process multiple files at the same time if multithreaded option is set (-T parameter larger than 1)
- if($fileA ne "TAB" && $thread > 1){
- my $thr = threads->create(\&generateInputFiles, $library, $fileA, $fileB, $extending, $reverse, $fname, $ctlib);
- if(!($ctlib % $thread)){
- foreach my $thr (threads->list()) {
- my @res = $thr->join();
- ($lib,$nreads,$ncount) = split(/,/,$res[0]);
- $libResHash->{$lib}{'reads'}+=$nreads;
- $libResHash->{$lib}{'N'}+=$ncount;
- }
- }
- #otherwise, process only one file at a time
- }elsif($fileA ne "TAB" && $thread <=1){
- my $out = &generateInputFiles($library, $fileA, $fileB, $extending, $reverse, $fname, $ctlib);
- ($lib,$nreads,$ncount) = split(/,/,$out);
- $libResHash->{$lib}{'reads'}+=$nreads;
- $libResHash->{$lib}{'N'}+=$ncount;
- }
- #if user has inserted a TAB file, calculate read statistics
- if($fileA eq "TAB"){
- open FILE, "$fileB" or die $!;
- my ($fileBaseName2, $dirName2, $fileExtension2) = fileparse($fileB);
- print "Reading tabfile: $fileBaseName2...\n";
- $counter2++ while(<FILE>);
- $libResHash->{$lib}{'reads'}+=$counter2;
- $libResHash->{$lib}{'N'} = 0;
- close FILE;
- }
- $prevlibrary = $library;
- }
- #Process remaining reads
- if($fileA ne "TAB"){
- foreach my $thr (threads->list()) {
- my @res = $thr->join();
- ($lib,$nreads,$ncount) = split(/,/,$res[0]);
- $libResHash->{$lib}{'reads'}+=$nreads;
- $libResHash->{$lib}{'N'}+=$ncount;
- }
- }
- #Print read statistics to the summary file
- &printMessage("\n$seplines");
- foreach my $libs (keys %$libResHash){
- my $totcounter = $libResHash->{$libs}{'reads'};
- my $totNcount = $libResHash->{$libs}{'N'};
- my $filt = $totcounter-$totNcount;
- print SUMFILE "READING READS $libs:\n";
- print SUMFILE "$seplines\tTotal inserted pairs = $totcounter \n";
- print SUMFILE "\tNumber of pairs containing N's = $totNcount \n\tRemaining pairs = $filt\n$seplines\n";
- }
- close FILELIB;
- close SUMFILE;
- close LOG;
-
- mkpath('process_OK'); #make directory, indicating that process has run OK
-
-#--------------------------------------------------
-
-###CONVERT INPUT SEQUENCES BY REMOVING PAIRED READS HAVING AN 'N'
-sub generateInputFiles{
- my ($lib, $fileA, $fileB, $extension, $reverse, $fname, $libct) = @_;
- my ($name,$seq1,$seq2, $res1,$res2);
- my ($counterext, $Ncount, $countsinglet, $fastq, $step) = (0,0,0,0,1000000);
- open (OUTSINGLEFILE, ">reads/$base_name.$lib.file$libct.fa") || die "Can't write to single file file$fname-- fatal\n";
-
- #check if file is fastQ or fastA
- open(TEST, "< $fileA");
- $name = <TEST>;
- close TEST;
- $fastq = 1 if ($name =~ /^[@]/);
-
- open(FILEA, "< $fileA");
- open(FILEB, "< $fileB");
- CounterPrint("Reading read-pairs $lib.$libct @ $countsinglet ");
- while(<FILEA>) {
- <FILEB>;
- $seq1 = uc(<FILEA>), $seq1 =~ s/^\r\n/\n/;
- $seq2 = uc(<FILEB>), $seq2 =~ s/^\r\n/\n/;
- #FASTQ FORMAT
- <FILEA>,<FILEA>,<FILEB>,<FILEB> if ($fastq);
-
- $res1 = index($seq1,"N");
- $res2 = index($seq2,"N");
- #if both reads contain N's, do not use them for contig extension and for scaffolding
- if($res1 == -1 && $res2 == -1){
- print OUTSINGLEFILE ">read$countsinglet/1\n$seq1>read$countsinglet/2\n$seq2";
- }else{
- $Ncount++;
- }
- if(++$countsinglet == $step){
- CounterPrint("Reading read-pairs $lib.$libct @ $countsinglet ");
- $step = $step + 1000000;
- }
-
- }
- CounterPrint("\n") if($thread <= 1);
- CounterPrint((" " x 40));
- close OUTSINGLEFILE;
- close FILEB;
- close FILEA;
- return "$lib,$countsinglet,$Ncount";
-}
-
-#------------------READ UNPAIRED SINGLE READS FILE WHEN -u IS SET
-
-sub readUnpairedFile{
- my ($file) = @_;
- open(INUNPAIRED, "< $file") || die "Can't open $file -- fatal\n";
- open OUTFILEExt, "> reads/$filenameOutExt";
-
- &printMessage("\n=>".getDate().": Reading, filtering and converting unpaired input sequences initiated\n");
-
- my ($seq1, $name);
- my ($counterext, $counter, $step, $fastq) = (0,0, 100000,0);
-
- open(TEST, "< $file");
- $name = <TEST>;
- close TEST;
- $fastq = 1 if ($name =~ /^[@]/);
- while(<INUNPAIRED>) {
- $seq1 = uc(<INUNPAIRED>); $seq1 =~ s/\r\n/\n/; chomp $seq1;
-
- #FASTQ FORMAT
- if ($fastq){
- <INUNPAIRED>; <INUNPAIRED>;
- }
- # ELSE FASTA FORMAT
- if(index($seq1, "N") == -1){
- print OUTFILEExt ">$counterext\n$seq1\n";
- $counterext++;
- }
- if(++$counter == $step){
- CounterPrint($counter);
- $step = $step + 100000;
- }
- }
- CounterPrint(" ");
-
- print SUMFILE "READING UNPAIRED READS:\n";
- print SUMFILE "$seplines\tTotal inserted reads = $counter \n";
- print SUMFILE "\tNumber of reads containing N's = ".($counter-$counterext)."\n\tRemaining reads = $counterext\n";
- close OUTFILEext;
- close INUNPAIRED;
-}
-
-###FUNCTION TO REVERSE COMPLEMENT A SEQUENCE
-sub reverseComplement{
- $_ = shift;
- tr/ATGC/TACG/;
- return (reverse());
-}
-
-###PRINTS A COUNTER ON THE SCREEN AND OVERWRITES PREVIOUS LINE
-sub CounterPrint{
- my $countingMessager = shift;
- print "\r$countingMessager";
- $|++;
-}
-
-###FUNCTION TO PRINT MESSAGES TO THE SCREEN AND TO THE LOG FILE
-sub printMessage{
- my $message = shift;
- print $message;
- print LOG $message;
-}
-
-###FUNCTION TO GET THE CURRENT DATE
-sub getDate{
- my $date = scalar(localtime);
- return $date;
-}
-
-###FLUSHES THE SUMMARY AND LOG FILE
-sub FlushFiles{
- select((select(SUMFILE), $| = 1)[0]);
- select((select(LOG), $| = 1)[0]);
- $|++;
-}
-
-#########END readLibFiles.pl
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/sspace/bowtie/VERSION b/external/gatb-minia-pipeline/sspace/bowtie/VERSION
deleted file mode 100755
index 679934348d0b19af6ec8588884c251d795fabf10..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/bowtie/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-0.12.5
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/sspace/bowtie/bowtie b/external/gatb-minia-pipeline/sspace/bowtie/bowtie
deleted file mode 100755
index 58eea317f3861917843dd606980d623bec49ec7d..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/sspace/bowtie/bowtie and /dev/null differ
diff --git a/external/gatb-minia-pipeline/sspace/bowtie/bowtie-build b/external/gatb-minia-pipeline/sspace/bowtie/bowtie-build
deleted file mode 100755
index 4b135619f1a1df6132a9ad80a5febfc69f15a30a..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/sspace/bowtie/bowtie-build and /dev/null differ
diff --git a/external/gatb-minia-pipeline/sspace/bowtie/bowtie-build-debug b/external/gatb-minia-pipeline/sspace/bowtie/bowtie-build-debug
deleted file mode 100755
index 5d0c970c8e45cf920ab6a7c0278431f87e2e1d64..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/sspace/bowtie/bowtie-build-debug and /dev/null differ
diff --git a/external/gatb-minia-pipeline/sspace/dotlib/DotLib.pm b/external/gatb-minia-pipeline/sspace/dotlib/DotLib.pm
deleted file mode 100755
index 24d774647080b8e903b1968f73a085df05d3d8ed..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/dotlib/DotLib.pm
+++ /dev/null
@@ -1,238 +0,0 @@
-# $Id: DotLib.pm,v 1.3 2003/02/24 17:33:00 mpop Exp $
-#
-# DotLib.pm - set of procedures for generating .dot files
-#
-
-# Copyright @ 2002, 2003, The Institute for Genomic Research (TIGR). All
-# rights reserved.
-
-
-=head1 Name
-
-DotLib - library of routines for generating .dot files
-
-=head1 Synopsis
-
- use DotLib;
-
-=head1 Description
-
- A set of procedures used to create various .dot objects such as
-file headers, file tails, components, nodes, edges, etc.
-
-=cut
-
-package DotLib;
-
-use strict;
-
-
-BEGIN {
- use Exporter ();
- use vars qw(@EXPORT @EXPORT_OK @ISA %EXPORT_TAGS);
-
- @ISA = qw(Exporter);
- @EXPORT = qw(&printHeader
- &printFooter
- &printNode
- &printEdge
- &startCluster
- &endCluster
- );
- %EXPORT_TAGS = ();
- @EXPORT_OK = ();
-}
-
-our $VERSION = '1.0';
-our $REVISION = '$Revision: 1.3 $ ';
-our $VERSION_STRING = "$VERSION ($REVISION)";
-
-use vars @EXPORT;
-use vars @EXPORT_OK;
-
-=over 4
-
-=item B<my $ret = printHeader($file, $type);>
-
-Prints a .dot header for the type of output specified in the $type variable.
-Allowable types are "printer", "plotter". If $type is undefined or not
-passed, it generates a default header. Returns 1 upon successful
-completion and 'undef' otherwise.
-
-Example:
-
- my $err = printHeader(\*STDOUT, "plotter");
-
-=cut
-
-sub printHeader
-{
- my $file = shift;
- my $type = shift;
-
- print $file "digraph ROOT {\n";
- print $file " rankdir = LR\n";
- print $file " orientation = landscape\n";
- print $file " ranksep = 0.3\n";
- print $file " nodesep = 0.3\n";
- print $file " fontsize = 8\n";
- print $file " margin = \".2,.2\"\n";
-
- if ($type eq "printer"){
- print $file " ratio = auto\n";
- print $file " page = \"8.5,11\"\n";
- } elsif ($type eq "plotter"){
- print $file " ratio = auto\n";
- print $file " page = \"36,48\"\n";
- }
-
- print $file "\n";
-
- return 1;
-} # printHeader
-
-
-=item B<my $ret = printFooter($file);>
-
-Prints a .dot footer (currently just a closed brace). Returns 1 upon
-successful completion and 'undef' otherwise.
-
-Example:
-
- my $err = printFooter(\*STDOUT);
-
-=cut
-
-sub printFooter
-{
- my $file = shift;
-
- print $file "}\n";
-
- return 1;
-} # printFooter
-
-
-=item B<my $ret = printNode($file, $id, $label, $ori);>
-
-Prints a "contig" node with the specified id, label, and orientation.
-If orientation is 1 then the node is a forward facing arrow, otherwise
-it is a backward facing arror. Returns 1 upon successful completion
-and 'undef' otherwise.
-
-Example:
-
- my $err = printNode(\*STDOUT, $node_id, "$node_id ($node_len)", 1);
-
-=cut
-
-sub printNode
-{
- my $file = shift;
- my $id = shift;
- my $label = shift;
- my $ori = shift;
- my $angle;
-
- $id =~ s/(\W)/_/g;
-
- if ($ori == 1){
- $angle = -90;
- } else {
- $angle = 90;
- }
-
- print $file " $id [ label = \"$label\" height = 0.2, fontsize = 8, shape = \"house\", orientation = $angle ]\n";
-
- return 1;
-
-} # printNode
-
-
-=item B<my $ret = printEdge($file, $nodeA, $nodeB, $label, $style);>
-
-Prints an edge between two nodes with the specified label. The style can
-be any of the GraphViz acceptable styles ("dotted", "solid", "dashed",
-"invis") or undefined in which case the default is used. Returns 1 upon
-successful completion and 'undef' otherwise.
-
-Example:
-
- my $err = printEdge(\*STDOUT, $nodeA, $nodeB, "A to B", "invis");
-
-=cut
-
-sub printEdge
-{
- my $file = shift;
- my $nodeA = shift;
- my $nodeB = shift;
- my $label = shift;
- my $instyle = shift;
- my $style;
-
- $nodeA =~ s/(\W)/_/g;
- $nodeB =~ s/(\W)/_/g;
-
- if (defined $instyle){
- $style = "style = \"" . $instyle . "\"";
- if ($instyle eq "invis"){
- $style .= " color = \"white\" ";
- }
- }
-
- print $file " $nodeA -> $nodeB [ label =\"$label\" fontsize = 8 $style ]\n";
-
- return 1;
-} # printEdge
-
-=item B<my $err = startCluster($file, $id, $label);>
-
-Starts a cluster in the .dot output file with the given label and id.
-Returns 1 upon successful completion and 'undef' otherwise.
-
-Example:
-
- my $err = startCluster(\*STDOUT, $clust_id, "first cluster");
-
-=cut
-
-sub startCluster
-{
- my $file = shift;
- my $id = shift;
- my $label = shift;
-
- $id =~ s/(\W)/_/g;
-
- print $file " subgraph cluster_$id {\n";
- print $file " label = \"$label\"\n";
-
- return 1;
-} # startCluster
-
-=item B<my $err = endCluster($file);>
-
-Ends a cluster in the .dot output. Returns 1 upon successful
-completion and 'undef' otherwise.
-
-Example:
-
- my $err = endCluster(\*STDOUT);
-
-=cut
-
-sub endCluster
-{
- my $file = shift;
-
- print $file " }\n";
-
- return 1;
-} # endCluster
-
-
-1;
-
-
-
diff --git a/external/gatb-minia-pipeline/sspace/tools/TQS.py b/external/gatb-minia-pipeline/sspace/tools/TQS.py
deleted file mode 100755
index e0b1a25dfb4c6fcb159a189ce2c548f8a99d9dcf..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/TQS.py
+++ /dev/null
@@ -1,218 +0,0 @@
-#!/usr/bin/env python
-
-__doc__ = """
-TQS
-
-Trim Quality Solexa Sequences (TQS)
-
-SYNOPSIS
- Quality trim solexa-Illumina sequence reads using user-defined thresholds
-"""
-__author__ = "Rene L. Warren"
-__version__ = '1.0'
-
-#LICENSE
-# Copyright (c) 2007 Canada's Michael Smith Genome Science Centre. All rights reserved.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-import sys, os, re, string
-from datetime import datetime
-from optparse import OptionParser
-
-
-def main():
- usage = "Usage: %s --help"
-
- parser = OptionParser()
- parser.add_option("-f", "--sequence file", dest="seqfile",
- help="Illumina sequence file - Output format from the 1G Genome Analyzer (_seq.txt): 7 1 255 669 AACCCCCACTCCTACAACGCCATCATTCCCCTCGAC",)
- parser.add_option("-q", "--qual file", dest="qualfile",
- help="A prb file containing all the Illumina intensities, as outputted by the 1G Genome Analyzer (_prb.txt)",)
- parser.add_option("-l", "--length", dest="mer", type="int", default=36,
- help="Length of sequence reads (i.e. Number of sequencing cycles, default=36)",)
- parser.add_option("-t", "--threshold", dest="threshold", type="int", default=5,
- help="Base intensity threshold value (-40 to 40, default=5)",)
- parser.add_option("-d", "--difference", dest="diff", type="int", default=5,
- help="Base intensity difference between top intensity and second best (1 to 80, default=5)",)
- parser.add_option("-c", "--consec", dest="consec", type="int", default=20,
- help="Minimum number of consecutive bases passing threshold values (default=20)",)
- parser.add_option("-v", "--verbose", dest="verbose", action="store_true",
- help="Runs in Verbose mode.",)
- (opts, args) = parser.parse_args()
-
- try:
- f = open(opts.seqfile)
- seq = f.readlines()
- f.close()
- except Exception, e:
- print "ERROR: Could not read from %s: %s" % (opts.seqfile, e)
- print usage % (sys.argv[0:])
- sys.exit()
-
- try:
- f = open(opts.qualfile)
- qual = f.readlines()
- f.close()
- except Exception, e:
- print "ERROR: Could not read from %s: %s" % (opts.qualfile, e)
- print usage % (sys.argv[0:])
- sys.exit()
-
-
- fasta = "%s_I%sD%sL%s.trim.fa" % (opts.seqfile,opts.threshold,opts.diff,opts.consec)
- log = "%s.log" % opts.seqfile
-
-
- try:
- FASTA = open(fasta, 'w')
- except:
- print "ERROR: Can not write to %s" % fasta
- sys.exit()
-
- try:
- LOG = open(log, 'w')
- except:
- print "ERROR: Can not write to %s" % log
- sys.exit()
-
-
- if opts.mer < 15 or opts.mer > 200:
- print "ERROR: -l must be a number between 15 and 200."
- sys.exit()
-
- if opts.consec < 16 or opts.consec > opts.mer:
- print "ERROR: -c must be a number between 16 and -l."
- sys.exit()
-
- LOG.write("""
-Running:
-%s
--f %s
--q %s
--l %s
--c %s
--t %s
--d %s
-Fasta file: %s
-
-""" % (sys.argv[0:],opts.seqfile, opts.qualfile, opts.mer, opts.consec, opts.threshold, opts.diff, fasta))
-
- t0 = datetime.now()
- LOG.write("\nReading Quality File: %s\n" % str(t0)[:len('2006-10-05 23:04')])
- trim_info = parseQualFile(opts.threshold, opts.diff, opts.consec, opts.mer, qual, opts.verbose, LOG)
- t1 = datetime.now()
- LOG.write("\n\nTrimming low quality bases: %s\n" % str(t1)[:len('2006-10-05 23:04')])
- readNTrim(trim_info, seq, opts.verbose, FASTA, LOG)
- LOG.write("DNA sequences have been trimmed accordingly and placed in %s" % fasta)
-
- LOG.close()
- FASTA.close()
- return
-
-#--------------------------------------------------------------------------------------
-def parseQualFile(threshold, difference, consecutive, read_length, qual, verbose, LOG):
- """
- Parse a solexa-illumina intensity file
-
- Return a Dictionary of sequence order number, with the index value and length to extract
- """
- trim_info = {}
- ok_read = 0
- read_number = 0
-
- if verbose:
- print "Printing trimming pattern for all reads passing the set threshold values...\n"
-
- for line in qual:
- read_number += 1 ### this keeps track of the read order, respected between the prb and seq files
- concat = "" ### concat builds a string of bases passing the user-defined filter
- quartets = line.split("\t") ### split quartet (4 number per position)
- for quartet in quartets: ### cycle through each quartet
- quad = (quartet.split())
- quadint = []
- for basequal in quad: ### each intensity/number for each position
- quadint.append(int(basequal))
- quadint.sort()
- quadint.reverse()
- basediff = quadint[0] - quadint[1]
- #print "T=%i D=%i" % (quadint[0],basediff)
-
- if quadint[0] < threshold or basediff < difference:
- concat += "x"
- else:
- concat += "-"
-
- head_match_regex = re.compile("\-{%i,%i}" % (consecutive,read_length))
- head_match = head_match_regex.search(concat)
- if head_match != None:
- ok_read += 1
- col = head_match.span()
- if not trim_info.has_key(read_number):
- trim_info[read_number] = {}
-
- start = int(col[0])
- end = int(col[1])
-
- trim_info[read_number]['start'] = start
- trim_info[read_number]['end'] = end
-
- if verbose:
- sub = concat[trim_info[read_number]['start']:trim_info[read_number]['end']]
- print "passed seqs:%i line#%i %s (start trim:%i,length:%i) %s\n" % (ok_read, read_number, concat, start, end, sub)
-
- LOG.write("%i out of %i sequences passed your filter (I >= %i and D >= %i and L >= %i)\n" % (ok_read, read_number, threshold, difference, consecutive))
-
- return trim_info
-
-
-#--------------------------------------------------------------------------------------
-def readNTrim(trim_info, seq, verbose, FASTA, LOG):
-
- """
- Parse a solexa/illumina sequence file and trim DNA sequence based user-defined intensity threshold/differences
- """
-
-
- read_number = 0
- gDNAlinker_count = 0
- usable_reads = 0
-
- dna_sequence_field = re.compile('^[ACTG]+$')
- gDNAlinker1_field = re.compile('^ATCCCC[GA]A')
- gDNAlinker2_field = re.compile('^ATCTAACAG')
-
- if verbose:
- print "Printing trimmed sequences for all reads passing the set threshold values minus, excluding sequence containing linkers...\n"
-
- for line in seq:
- read_number += 1 ### tracks read number / will match order in prb file
- line = line.rstrip('\r\n')
- info = line.split("\t") ### split line, the seq file lists: lane tile xcoord y coord DNAseq
- dna_string = info[4]
-
- if trim_info.has_key(read_number):
- trim_seq = dna_string[trim_info[read_number]['start']:trim_info[read_number]['end']]
- if re.match(dna_sequence_field, trim_seq): ### no ambiguous bases?
- if re.match(gDNAlinker1_field, trim_seq) or re.match(gDNAlinker2_field,trim_seq): ### matches gDNA linker?
- gDNAlinker_count += 1
- else:
- usable_reads += 1
- FASTA.write(">%s-%s-%s-%s\n%s\n" % (info[0],info[1],info[2],info[3],trim_seq))
- if verbose:
- print "line#%i %s (start trim:%i,length:%i) %s" % (read_number,info[4],trim_info[read_number]['start'],trim_info[read_number]['end'],trim_seq)
- LOG.write("%i out of %i sequences appear to be usable, after filtering out sequences hard-coded in this program * %i gDNA linker sequences*\n" % (usable_reads, read_number,gDNAlinker_count))
- return
-
-if __name__ == '__main__':
- main()
- import time
- sys.exit()
diff --git a/external/gatb-minia-pipeline/sspace/tools/TQS.readme b/external/gatb-minia-pipeline/sspace/tools/TQS.readme
deleted file mode 100755
index fc633d464d4ee1914df4974cb8545d6f2100316c..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/TQS.readme
+++ /dev/null
@@ -1,63 +0,0 @@
-
-TQS
-
-Trim Quality Solexa-Illumina Sequences (TQS)
-
-SYNOPSIS
- Quality trim solexa-Illumina sequence reads using user-defined thresholds
-"""
-__author__ = "Rene L. Warren"
-__version__ = '1.0'
-
-#LICENSE
-# Copyright (c) 2007 Canada's Michael Smith Genome Science Centre. All rights reserved.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-Execution example
-==================
-python TQS.py -f test_seq.txt -q test_prb.txt -l 36 -t 5 -d 5 -c 20
-
-
-Options
-=======
-python TQS.py --help
-
-Usage: TQS.py [options]
-
-Options:
- -h, --help show this help message and exit
- -f SEQFILE, --sequence file=SEQFILE
- Illumina sequence file - Output format from the 1G
- Genome Analyzer (_seq.txt):
- 7 1 255 669
- AACCCCCACTCCTACAACGCCATCATTCCCCTCGAC
- -q QUALFILE, --qual file=QUALFILE
- A prb file containing all the Illumina intensities, as
- outputted by the 1G Genome Analyzer (_prb.txt)
- -l MER, --length=MER Length of sequence reads (i.e. Number of sequencing
- cycles, default=36)
- -t THRESHOLD, --threshold=THRESHOLD
- Base intensity threshold value (-40 to 40, default=5)
- -d DIFF, --difference=DIFF
- Base intensity difference between top intensity and
- second best (1 to 80, default=5)
- -c CONSEC, --consec=CONSEC
- Minimum number of consecutive bases passing threshold
- values (default=20)
- -v, --verbose Runs in Verbose mode.
-
-
-Output
-======
-
-.log file: Indicates the option chosen and tracks the execution time
-.fa file: A single fasta file containing the sequence reads that passed the filter specified
diff --git a/external/gatb-minia-pipeline/sspace/tools/TQSexport.py b/external/gatb-minia-pipeline/sspace/tools/TQSexport.py
deleted file mode 100755
index 3adef4acb0d572a525b569620344b6c0a469cdca..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/TQSexport.py
+++ /dev/null
@@ -1,164 +0,0 @@
-#!/usr/bin/env python
-
-__doc__ = """
-TQS
-
-Trim Quality Solexa Sequences (TQS)
-
-SYNOPSIS
- Quality trim solexa-Illumina sequence reads using user-defined thresholds
-"""
-__author__ = "Rene L. Warren"
-__version__ = '1.0'
-
-#LICENSE
-# Copyright (c) 2007 Canada's Michael Smith Genome Science Centre. All rights reserved.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-import sys, os, re, string, math
-from datetime import datetime
-from optparse import OptionParser
-
-
-def main():
- usage = "Usage: %s --help"
-
- parser = OptionParser()
- parser.add_option("-f", "--export file", dest="exportfile",
- help="Illumina export file - Output format from the Genome Analyzer",)
- parser.add_option("-t", "--Phred quality threshold", dest="threshold", type="int", default=10,
- help="Base intensity threshold value (Phred quality scores 0 to 40, default=10)",)
- parser.add_option("-c", "--consec", dest="consec", type="int", default=20,
- help="Minimum number of consecutive bases passing threshold values (default=20)",)
- parser.add_option("-v", "--verbose", dest="verbose", action="store_true",
- help="Runs in Verbose mode.",)
- (opts, args) = parser.parse_args()
-
- try:
- f = open(opts.exportfile)
- seq = f.readlines()
- f.close()
- except Exception, e:
- print "ERROR: Could not read from %s: %s" % (opts.exportfile, e)
- print usage % (sys.argv[0:])
- sys.exit()
-
-
- fasta = "%s_T%sC%s.trim.fa" % (opts.exportfile,opts.threshold,opts.consec)
- log = "%s.log" % opts.exportfile
- minimum_length = 15
-
-
- try:
- FASTA = open(fasta, 'w')
- except:
- print "ERROR: Can not write to %s" % fasta
- sys.exit()
-
- try:
- LOG = open(log, 'w')
- except:
- print "ERROR: Can not write to %s" % log
- sys.exit()
-
- if opts.consec < minimum_length:
- print "ERROR: -c must be a number larger than %i." % (minimum_length)
- sys.exit()
-
- LOG.write("""
-Running:
-%s
--f %s
--c %s
--t %s
-Fasta file: %s
-
-""" % (sys.argv[0:],opts.exportfile, opts.consec, opts.threshold, fasta))
-
- t1 = datetime.now()
- LOG.write("\n\nTrimming low quality bases: %s\n" % str(t1)[:len('2006-10-05 23:04')])
- readNtrim(seq, opts.threshold, opts.consec, opts.verbose, FASTA, LOG)
- LOG.write("DNA sequences have been trimmed accordingly and placed in %s" % fasta)
-
- LOG.close()
- FASTA.close()
- return
-
-#--------------------------------------------------------------------------------------
-def readNtrim(export, threshold, consecutive, verbose, FASTA, LOG):
- """
- Parse a solexa-illumina export file
- SOLEXA3_77_30V9CAAXX 4 1 1068 522 1 GGACAGCTGACAGCTGTTAAGAAGGACCCTATGTTAAAGGAAATGGATAC YYYYYYYYYYYJYY
-YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr13 36311743 F 50 52 121 187 R N
- Return a Dictionary of sequence order number, with the index value and length to extract
- """
- trim_info = {}
- ok_read = 0
- read_number = 0
-
- if verbose:
- print "Printing trimming pattern for all reads passing the set threshold values...\n"
-
- for line in export:
- read_number += 1
- concat = "" ### concat builds a string of bases passing the user-defined filter
- info = line.split() ### split info
- illumina_encoded_qual = list(info[7])
- """
- print "line%s\tseq:%s\tqual:%s\n" % (line,info[6],info[7])
- """
- pos = 0
- for illumina_qual in illumina_encoded_qual:
- pos += 1
- Q = 10 * math.log(1 + 10 ** ((ord(illumina_qual) - 64) / 10.0)) / math.log(10)
- if Q < threshold:
- concat += "x"
- else:
- concat += "-"
- """
- print "base#%i. Illumina qual (%s) == phredQ (%i)\n" % (pos,illumina_qual,Q)
- """
-
- seq_len = len(info[6])
- head_match_regex = re.compile("\-{%i,%i}" % (consecutive, seq_len))
- head_match = head_match_regex.search(concat)
- if head_match != None:
- ok_read += 1
- col = head_match.span()
- if not trim_info.has_key(read_number):
- trim_info[read_number] = {}
-
- start = int(col[0])
- end = int(col[1])
-
- pair = ""
- if info[5] == "1":
- pair = "a"
- elif info[5] == "2":
- pair = "b"
-
- trim_seq = info[6][start:end]
- FASTA.write(">%s-%s-%s-%s%s\n%s\n" % (info[1],info[2],info[3],info[4],pair,trim_seq))
-
- if verbose:
- print "passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (ok_read, read_number, concat, start, end, trim_seq)
-
- LOG.write("%i out of %i sequences passed your filter (-t >= %i and -c >= %i)\n" % (ok_read, read_number, threshold, consecutive))
-
- return
-
-
-
-if __name__ == '__main__':
- main()
- import time
- sys.exit()
diff --git a/external/gatb-minia-pipeline/sspace/tools/TQSfastq.py b/external/gatb-minia-pipeline/sspace/tools/TQSfastq.py
deleted file mode 100755
index a8dcb047da53bd10ca2ff72ee2266114658427a9..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/TQSfastq.py
+++ /dev/null
@@ -1,174 +0,0 @@
-#!/usr/bin/env python
-
-__doc__ = """
-TQS
-
-Trim Quality Sequences (TQS)
-
-SYNOPSIS
- Quality trim FASTQ sequence reads using user-defined thresholds
-"""
-__author__ = "Rene L. Warren"
-__version__ = 'fastq'
-
-#LICENSE
-# Copyright (c) 2007 Canada's Michael Smith Genome Science Centre. All rights reserved.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# Modified by Lance Parsons at Princton University's Lewis-Sigler Institute for Integrative Genomics
-# Adapted to trim "standard" FASTQ files (PHRED+33)
-
-import sys, os, re, string, math
-from datetime import datetime
-from optparse import OptionParser
-
-
-def main():
- usage = "Usage: %s --help"
-
- parser = OptionParser()
- parser.add_option("-f", "--fastq file", dest="fastqfile",
- help="fastq (fq) file - standard (ASCII+33) encoded PHRED quality scores / illumina (ASCII+64) encoded PHRED quality scores",)
- parser.add_option("-t", "--Phred quality threshold", dest="threshold", type="int", default=10,
- help="Base intensity threshold value (Phred quality scores 0 to 40, default=10)",)
- parser.add_option("-c", "--consec", dest="consec", type="int", default=20,
- help="Minimum number of consecutive bases passing threshold values (default=20)",)
- parser.add_option("-e", "--ASCII encoding type: 33 or 64", dest="encoding", type="int", default=64,
- help="Type of ASCII encoding: 33 (standard) or 64 (illumina) (default=64)",)
- parser.add_option("-v", "--verbose", dest="verbose", action="store_true",
- help="Runs in Verbose mode.",)
- (opts, args) = parser.parse_args()
-
- try:
- f = open(opts.fastqfile)
- seq = f.readlines()
- f.close()
- except Exception, e:
- print "ERROR: Could not read from %s: %s" % (opts.fastqfile, e)
- print usage % (sys.argv[0:])
- sys.exit()
-
-
- fasta = "%s_T%sC%sE%s.trim.fa" % (opts.fastqfile, opts.threshold, opts.consec, opts.encoding)
- log = "%s.log" % opts.fastqfile
- minimum_length = 15
-
-
- try:
- FASTA = open(fasta, 'w')
- except:
- print "ERROR: Can not write to %s" % fasta
- sys.exit()
-
- try:
- LOG = open(log, 'w')
- except:
- print "ERROR: Can not write to %s" % log
- sys.exit()
-
- if opts.consec < minimum_length:
- print "ERROR: -c must be a number larger than %i." % (minimum_length)
- sys.exit()
-
- if opts.encoding != 33 and opts.encoding != 64:
- print "ERROR: -e must be either 33 or 64."
- sys.exit()
-
- LOG.write("""
-Running:
-%s
--f %s
--c %s
--t %s
--e %s
-Fasta file: %s
-
-""" % (sys.argv[0:], opts.fastqfile, opts.consec, opts.threshold, opts.encoding, fasta))
-
- t1 = datetime.now()
- LOG.write("\n\nTrimming low quality bases: %s\n" % str(t1)[:len('2006-10-05 23:04')])
- readNtrim(seq, opts.threshold, opts.consec, opts.encoding, opts.verbose, FASTA, LOG)
- LOG.write("DNA sequences have been trimmed accordingly and placed in %s" % fasta)
-
- LOG.close()
- FASTA.close()
- return
-
-#--------------------------------------------------------------------------------------
-def readNtrim(fastq, threshold, consecutive, encoding, verbose, FASTA, LOG):
- """
- Return a Dictionary of sequence order number, with the index value and length to extract
- """
- trim_info = {}
- ok_read = 0
- read_number = 0
- record_line = 0
-
- if verbose:
- print "Printing trimming pattern for all reads passing the set threshold values...\n"
-
- for line in fastq:
- record_line += 1
- if record_line == 1:
- read_id = line.strip()
- elif record_line == 2:
- seq = line.strip()
- elif record_line == 3:
- qual_id = line.strip()
- elif record_line == 4:
- record_line = 0
- qual = line.strip()
- read_number += 1
- concat = "" ### concat builds a string of bases passing the user-defined filter
- """
- print "line%s\tseq:%s\tqual:%s\n" % (line,info[6],info[7])
- """
- pos = 0
- for qual_char in qual:
- Q = (ord(qual_char) - encoding)
- pos += 1
- if Q < threshold:
- concat += "x"
- else:
- concat += "-"
- """
- print "base#%i. Illumina qual (%s) == phredQ (%i)\n" % (pos,illumina_qual,Q)
- """
-
- seq_len = len(seq)
- head_match_regex = re.compile("\-{%i,%i}" % (consecutive, seq_len))
- head_match = head_match_regex.search(concat)
- if head_match != None:
- ok_read += 1
- col = head_match.span()
- if not trim_info.has_key(read_number):
- trim_info[read_number] = {}
-
- start = int(col[0])
- end = int(col[1])
-
- trim_seq = seq[start:end]
- FASTA.write(">%s\n%s\n" % (read_id, trim_seq))
-
- if verbose:
- print "%s\n%s\n%s\n passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (read_id,seq,qual,ok_read, read_number, concat, start, end, trim_seq)
-
- LOG.write("%i out of %i sequences passed your filter (-t >= %i and -c >= %i)\n" % (ok_read, read_number, threshold, consecutive))
-
- return
-
-
-
-if __name__ == '__main__':
- main()
- import time
- sys.exit()
diff --git a/external/gatb-minia-pipeline/sspace/tools/TRIMMING_PAIRED_READS.README b/external/gatb-minia-pipeline/sspace/tools/TRIMMING_PAIRED_READS.README
deleted file mode 100755
index dff64ad70b58d11e2e89214da6fd89023939b58d..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/TRIMMING_PAIRED_READS.README
+++ /dev/null
@@ -1,88 +0,0 @@
-December 2008/February 2010
-Rene Warren
-rwarren at bcgsc dot ca
-warrenlr at gmail dot com
-
-#--------------------------------
-To trim reads using fastq as input, run TQSfastq.py on both PE file:
-*Make sure you know whether your fastq file qual score were encoded ASCII+33 (standard) or ASCII+64 (illumina)
-
-for options run:
-./TQSfastq.py --help
-
-Usage: TQSfastq.py [options]
-
-Options:
- -h, --help show this help message and exit
- -f FASTQFILE, --fastq file=FASTQFILE
- fastq (fq) file - standard (ASCII+33) encoded PHRED
- quality scores / illumina (ASCII+64) encoded PHRED
- quality scores
- -t THRESHOLD, --Phred quality threshold=THRESHOLD
- Base intensity threshold value (Phred quality scores 0
- to 40, default=10)
- -c CONSEC, --consec=CONSEC
- Minimum number of consecutive bases passing threshold
- values (default=20)
- -e ENCODING, --ASCII encoding type: 33 or 64=ENCODING
- Type of ASCII encoding: 33 (standard) or 64 (illumina)
- (default=64)
- -v, --verbose Runs in Verbose mode.
-
-
-e.g.
-./qseq2fastq.pl s_3_1_0048_qseq.txt > s_3_1_0048_qseq.txt.fq
-./qseq2fastq.pl s_3_2_0048_qseq.txt > s_3_2_0048_qseq.txt.fq
-./TQSfastq.py -f s_3_1_0048_qseq.txt.fq -t 20 -c 36 -e 64
-./TQSfastq.py -f s_3_2_0048_qseq.txt.fq -t 20 -c 36 -e 64
-
-To join both for SSAKE's paired-end input, run:
-./makePairedOutput2UNEQUALfiles.pl s_3_1_0048_qseq.txt.fq_T20C36E64.trim.fa s_3_2_0048_qseq.txt.fq_T20C36E64.trim.fa
-
-This will create 2 files: paired.fa and unpaired.fa
-Run SSAKE: SSAKE -f paired.fa -g unpaired.fa -p 1
-
-#--------------------------------
-*For those not interested in trimming their reads, but interested in joining 2 equal-record fasta files:
-
-./qseq2fasta.pl s_3_1_0048_qseq.txt > file1.fa
-./qseq2fasta.pl s_3_2_0048_qseq.txt > file2.fa
-./makePairedOutput2EQUALfiles.pl file1.fa file2.fa
-
-#--------------------------------
-Many of you asked me whether you could trim paired-end (PE) Illumina reads with TQS.py
-The answer is yes. However, I never got a chance to conjure a formal script for PE reads - But I hacked
-a work-around trimming paired reads:
-
-
-
-1. run splitInput.pl (supplied in the ./tools directory) where all *_seq.txt and *_prb.txt are located:
-
-Usage: ./splitInput.pl <directory where all *_seq and *_prb are> <# Illumina cycles (read length)>
-
-
-2. run this perl one-liner to make a shell script:
-
-ls -la | perl -ne 'if(/(s_\d+_\d+)_seq.txt.new/){print "TQS.py -f $1_seq.txt.new -q $1_prb.txt.new -l * -t * -d * -c *\n"}' > runTQS.sh
-*replace stars with your values
-
-
-3. Run the shell script the above command created (will run TQS.py on ALL tiles, sequentially (why not farming the job on a compte cluster?!)
-
- chmod 755 runTQS.sh
- ./runTQS.sh
-
-
-4. Concatenate all trimmed reads
-
- cat s*.trim.fa > all_raw.fa
-
-
-5. Make the paired output (that will become the input for ssake3.2.1 -f)
-using the 2nd script supplied in this directory.
-
-./makePairedOutput.pl all_raw.fa
-
-
-As always, feel free to contact me if you have any questions.
-Rene
diff --git a/external/gatb-minia-pipeline/sspace/tools/estimate_insert_size.pl b/external/gatb-minia-pipeline/sspace/tools/estimate_insert_size.pl
deleted file mode 100755
index 9b1f65ee0b77635f48e282c07295604a23e700ad..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/estimate_insert_size.pl
+++ /dev/null
@@ -1,190 +0,0 @@
-###################################################################################################################
-#Marten Boetzer BaseClear B.v. 14-07-2011 #
-#SSPACE perl subscript samToTab_multi.pl #
-#This script; #
-# -Estimates median insert size by mapping paired-reads on contigs #
-# It goes through each contig and maps both reads, if a pair is mapped, #
-# the orientation and insert size is estimated. #
-# If sufficient pairs (given by the user) are found, the median insert size is #
-# estimated, as well as a file with the distribution is generated which can be #
-# used to visualize the insert size distribution. #
-# #
-# To run this script; #
-# perl estimate_insert_size.pl <contigfile> <readfile1> <readfile2> <number_of_pairs> <orientation_of_pairs> #
- #
-# Output is the median insert size and a file with distribution of the insert size. Also, number of pairs for #
-# each found orientation (FR, RF, FF and RR) are given. #
-###################################################################################################################
-
-use FindBin qw($Bin);
-use File::Path;
-use strict;
-my $contigfile = $ARGV[0];
-my $fileA = $ARGV[1];
-my $fileB = $ARGV[2];
-my $numpairs = $ARGV[3];
-my $orientation = $ARGV[4];
-
-die "ERROR: Can't find contig file: $contigfile -- fatal\n" if(! -e $contigfile);
-die "ERROR: Can't find read file: $fileA -- fatal\n" if(! -e $fileA);
-die "ERROR: Can't find read file: $fileB -- fatal\n" if(! -e $fileB);
-if($numpairs eq ''){
- print "WARNING: No number of pairs are given, using 10000 pairs instead\n";
- $numpairs = 10000;
-}
-if($orientation eq ''){
- print "WARNING: No orientation of the pairs is given, using orientation FR instead\n";
- $orientation = "FR";
-}
-die "ERROR: You've inserted $numpairs, which does not seem to be an valid number. Exiting.\n" if(!($numpairs>0) || !($numpairs =~ /^\d+$/));
-die "ERROR: Orientation must have length of 2 characters and should contain one of the following; FR, FF, FR or RF. You've inserted orientation of $orientation ...Exiting.\n" if(!(length($orientation) == 2) || !($orientation =~ /[FR][FR]/));
-
-print "\n";
-my $paircount = 0;
-my ($direction, $insertsize);
-mkpath('bowtieoutput');
-open (CONT, $contigfile) || die "Can't open contig file $contigfile\n";
-
-my ($seq,$name, $maxctg, $maxseq, $maxname)=("","",0,"","");
-my $contignum = 0;
-CONTIG:
-while (<CONT>) {
- chomp;
- $seq.=$_ if(eof(CONT));
- if (/\>(\S+)/ || eof(CONT)){
- if($seq ne ""){
- $contignum++;
- if(length($seq) > $maxctg){
- $maxctg = length($seq);
- $maxseq = $seq;
- $maxname = $name;
- }
- if(eof(CONT)){
- $seq = $maxseq;
- $name = $maxname;
- }
- if(eof(CONT)){
- print "now at contig $name = size".length($seq)."\n";
- open (BOWCONT, ">bowtieoutput/bowtie_input.fa");
- print BOWCONT ">$name\n$seq\n";
- close BOWCONT;
- ($paircount) = &mapWithBowtie($contignum,"bowtieoutput/bowtie_input.fa", $fileA, $fileB);
- last CONTIG if($paircount>=$numpairs);
- }
-
- $name = "";
- $seq = "";
- }
- $name = $1;
- }
- else {
- $seq .= $_;
- }
-}
-
-foreach my $d (keys %$direction){
- print "direction $d is found $direction->{$d} times\n";
-}
-my ($median_ins,$record) = (0,0);
-my $median_bin = int($paircount/2);
-open (CSV, ">distribution.txt") || die "Can't open distribution.txt for writing -- fatal";
-foreach my $is (sort {$a<=>$b} keys %$insertsize){
- for(my $i=0;$i<$insertsize->{$is};$i++){
- $record++;
- $median_ins = $is if($record >= $median_bin && $median_ins == 0);
- }
- print CSV "$is\t$insertsize->{$is}\n";
-}
-
-print "\nmedian = $median_ins\n\nSee the distribution in file 'distribution.txt'\n";
-
-
-sub mapWithBowtie{
- my ($fname,$contig, $fileA, $fileB) = @_;
- my $bowtieout = "contig$fname.bowtieIndex";
- my $Bin2 = substr($Bin, 0, -5);
- my $bowtiepath = "$Bin2"."/bowtie/bowtie";
- $bowtiepath =~ s/ /\\ /g;
- my $bowbuildpath = $bowtiepath."-build";
- system("$bowbuildpath $contig bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
-
- my $fastq = 0;
- open(TEST, "< $fileA");
- $name = <TEST>;
- close TEST;
- $fastq = 1 if ($name =~ /^[@]/);
-
- open(FILEA, "< $fileA");
- open(FILEB, "< $fileB");
-
- my $count=0;
- open (BOWIN, ">bowtieoutput/bowtiein.$fname.fa") || die "Can't write to single file bowtieoutput/bowtiein.$fname.fa-- fatal\n";
- while(<FILEA>) {
- <FILEB>;
- $count++;
- my $seq1 = <FILEA>;
- chomp $seq1;
- my $seq2 = <FILEB>;
- chomp $seq2;
- #FASTQ FORMAT
- <FILEA>,<FILEA>,<FILEB>,<FILEB> if ($fastq);
-
- print BOWIN ">read$count\n$seq1>read$count\n$seq2";
- if($count > $numpairs){
- close BOWIN;
- open(IN, "$bowtiepath -p 1 -v 0 -m 1 bowtieoutput/$bowtieout --suppress 6,7 -f bowtieoutput/bowtiein.$fname.fa --quiet|") || die "Can't open bowtie output -- fatal\n";
- my ($prevread, $prevline);
- while(my $line = <IN>){
- my @t1 = split(/\t/,$line);
- if($prevread eq $t1[0]){
- $paircount++;
- my @t2 = split(/\t/,$prevline);
- my ($start1, $start2, $end1,$end2);
-
- if($t1[1] eq "+"){
- $end1 = $t1[3] + length($t1[4]);
- $start1 = $t1[3];
- }
- else{
- $start1 = $t1[3] + length($t1[4]);
- $end1 = $t1[3];
- }
- if($t2[1] eq "+"){
- $end2 = $t2[3] + length($t2[4]);
- $start2 = $t2[3];
- }
- else{
- $start2 = $t2[3] + length($t2[4]);
- $end2 = $t2[3];
- }
- my ($dir1, $dir2);
- $dir1 = "F" if($start1 < $end1);
- $dir1 = "R" if($start1 > $end1);
- $dir2 = "F" if($start2 < $end2);
- $dir2 = "R" if($start2 > $end2);
- $direction->{"$dir1$dir2"}++ if($start1 < $start2);
- $direction->{"$dir2$dir1"}++ if($start2 < $start1);
- my $diff = abs($start2-$start1);
- if($orientation eq "$dir1$dir2" || $orientation eq "$dir2$dir1"){
- $insertsize->{$diff}++;
- }
- return $paircount if($paircount >= $numpairs);
- }
- $prevread = $t1[0];
- $prevline = $line;
- }
-
- close BOWIN;
- open (BOWIN, "bowtieoutput/bowtiein.$fname.fa") || die "Can't write to single file bowtieoutput/bowtiein.$name.fa-- fatal\n";
- }
- }
- print "count = $paircount\n";
- return $paircount;
-}
-
-###PRINTS A COUNTER ON THE SCREEN AND OVERWRITES PREVIOUS LINE
-sub CounterPrint{
- my $countingMessager = shift;
- print "\r$countingMessager";
- $|++;
-}
diff --git a/external/gatb-minia-pipeline/sspace/tools/fq_all2std.pl b/external/gatb-minia-pipeline/sspace/tools/fq_all2std.pl
deleted file mode 100755
index c5b016fc573c4bf7171247d252aa577a0c8f6117..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/fq_all2std.pl
+++ /dev/null
@@ -1,254 +0,0 @@
-#!/usr/local/bin/perl -w
-
-# Author: lh3
-
-use strict;
-use warnings;
-use Getopt::Std;
-use FindBin qw($Bin);
-
-my $usage = qq(
-Usage: fq_all2std.pl <command> <in.txt> <lane_qseq (only for SRF conversions)>
-
-Command: scarf2std Convert SCARF format to the standard/Sanger FASTQ
- fqint2std Convert FASTQ-int format to the standard/Sanger FASTQ
- sol2std Convert Solexa/Illumina FASTQ to the standard FASTQ
- fa2std Convert FASTA to the standard FASTQ
- fq2fa Convert various FASTQ-like format to FASTA
- sol2scarf Convert Solexa/Illumina FASTQ to the SCARF format
- qseq2srf Convert Solexa/Illumina qseq format to the SRF format
- qseqin2srf Convert Solexa/Illumina qseq + intensity/noise format to the SRF format
- instruction Explanation to different format
- example Show examples of various formats
-
-Note: Read/quality sequences MUST be presented in one line.
-\n);
-
-die($usage) if (@ARGV < 1);
-
-# Solexa->Sanger quality conversion table
-my @conv_table;
-for (-64..64) {
- $conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));
-}
-
-# parsing command line
-my $cmd = shift;
-my %cmd_hash = (scarf2std=>\&scarf2std, fqint2std=>\&fqint2std, sol2std=>\&sol2std, fa2std=>\&fa2std,
- sol2scarf=>\&sol2scarf, fq2fa=>\&fq2fa, qseq2srf=>\&qseq2srf,
- qseqin2srf=>\&qseqin2srf, example=>\&example, instruction=>\&instruction);
-if (defined($cmd_hash{$cmd})) {
- if ($cmd eq 'qseq2srf') {
- &qseq2srf($ARGV[1]);
- }
- elsif ($cmd eq 'qseqin2srf') {
- &qseqin2srf($ARGV[1]);
- }
- &{$cmd_hash{$cmd}};
-} else {
- die("** Unrecognized command $cmd");
-}
-
-sub fa2std {
- my %opts = (q=>25);
- getopts('q:', \%opts);
- my $q = chr($opts{q} + 33);
- warn("-- The default quality is set to $opts{q}. Use '-q' at the command line to change the default.\n");
- while (<>) {
- if (/^>(\S+)/) {
- print "\@$1\n";
- $_ = <>;
- print "$_+\n", $q x (length($_)-1), "\n";
- }
- }
-}
-
-sub fq2fa {
- while (<>) {
- if (/^@(\S+)/) {
- print ">$1\n";
- $_ = <>; print;
- <>; <>;
- }
- }
-}
-
-sub scarf2std {
- while (<>) {
- my @t = split(':', $_);
- my $name = join('_', @t[0..4]);
- print "\@$name\n$t[5]\n+\n";
- my $qual = '';
- @t = split(/\s/, $t[6]);
- $qual .= $conv_table[$_+64] for (@t);
- print "$qual\n";
- }
-}
-
-sub fqint2std {
- while (<>) {
- if (/^@/) {
- print;
- $_ = <>; print; $_ = <>; $_ = <>;
- my @t = split;
- my $qual = '';
- $qual .= $conv_table[$_+64] for (@t);
- print "+\n$qual\n";
- }
- }
-}
-
-sub sol2std {
- my $max = 0;
- while (<>) {
- if (/^@/) {
- print;
- $_ = <>; print; $_ = <>; $_ = <>;
- my @t = split('', $_);
- my $qual = '';
- $qual .= $conv_table[ord($_)] for (@t);
- print "+\n$qual\n";
- }
- }
-}
-
-sub sol2scarf {
- my $counter = 0;
- while (<>) {
- chomp;
- if (/^@/) {
- my $line = substr($_,1);
- if ($counter==0) {
- print "$line:";
- $counter+=1;
- }
- else {
- print "\n$line:";
- }
- }
- elsif (/^[+]/) {
- print ":";
- }
- else {
- print "$_";
- }
- }
- print "\n";
-}
-
-sub qseq2srf {
- die "This routine is currently out of order. Compatibility could only be guaranteed until GAP version 1.3
-Formerly it could be called as follows: fq_all2std.pl qseq2srf s_3_*_qseq.txt\n";
-
- my $arg = shift;
- system("$Bin/srf-conversions/illumina2srf $arg");
-}
-
-sub qseqin2srf {
- die "This routine is currently out of order. Compatibility could only be guaranteed until GAP version 1.3
-Formerly it could be called as follows: fq_all2std.pl qseq2srf -b s_3_*_qseq.txt
-
-If you want to re-implement it do not forget to complete the pre-processing steps of the cif intensities and cnf noise files.
-A) To generate the cif intensities files, go to the Lane folder in Intensities and type:
-for ((i=001;i<=120;i++));
-do /data/scripts/next-gen/convert_sequence_format/srf-conversions/cifToTxt -l <lane> -t \$i;
-done
-B) To generate the cnf noise files, go to the Lane folder in Intensities and type:
-for ((i=001;i<=120;i++));
-do /data/scripts/next-gen/convert_sequence_format/srf-conversions/cnfToTxt -l <lane> -t \$i;
-done\n";
- my $arg = shift;
- system("$Bin/srf-conversions/illumina2srf -b $arg");
-}
-
-sub instruction {
-
- print "
-FASTQ format is first used in the Sanger Institute, and therefore
-we take the Sanger specification as the standard FASTQ. Although
-Solexa/Illumina reads file looks pretty much like the standard
-FASTQ, they are different in that the qualities are scaled
-differently. In the quality string, if you can see a character
-with its ASCII code higher than 90, probably your file is in the
-Solexa/Illumina format.
-
-Sometimes we also use an integer, instead of a single character,
-to explicitly show the qualities. In that case, negative
-qualities indicates that Solexa/Illumina qualities are used.
-
-";
-
-}
-
-sub example {
- my $exam_scarf = '
-USI-EAS50_1:4:2:710:120:GTCAAAGTAATAATAGGAGATTTGAGCTATTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 19 23 23 23 18 23 23 23
-USI-EAS50_1:4:2:690:87:GTTTTTTTTTTTCTTTCCATTAATTTCCCTTT:23 23 23 23 23 23 23 23 23 23 23 23 12 23 23 23 23 23 16 23 23 9 18 23 23 23 12 23 18 23 23 23
-USI-EAS50_1:4:2:709:32:GAGAAGTCAAACCTGTGTTAGAAATTTTATAC:23 23 23 23 23 23 23 23 20 23 23 23 23 23 23 23 23 23 23 23 23 12 23 18 23 23 23 23 23 23 23 23
-USI-EAS50_1:4:2:886:890:GCTTATTTAAAAATTTACTTGGGGTTGTCTTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
-USI-EAS50_1:4:2:682:91:GGGTTTCTAGACTAAAGGGATTTAACAAGTTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 20 23 23 23 23 23 23 23 23 23 23 23 18 23 23 23 23
-USI-EAS50_1:4:2:663:928:GAATTTGTTTGAAGAGTGTCATGGTCAGATCT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
-';
-
- my $exam_fqint = '
-@4_1_912_360
-AAGGGGCTAGAGAAACACGTAATGAAGGGAGGACTC
-+4_1_912_360
-40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 40 40 40 40 40 40 40 40 40 26 40 40 14 39 40 40
-@4_1_54_483
-TAATAAATGTGCTTCCTTGATGCATGTGCTATGATT
-+4_1_54_483
-40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 40 40 40 28 40 40 40 40 40 40 16 40 40 5 40 40
-@4_1_537_334
-ATTGATGATGCTGTGCACCTAGCAAGAAGTTGCATA
-+4_1_537_334
-40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 29 40 40 33 40 40 33 40 40 33 31 40 40 40 40 18 26 40 -2
-@4_1_920_361
-AACGGCACAATCCAGGTTGATGCCTACGGCGGGTAC
-+4_1_920_361
-40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 31 40 40 40 40 40 40 15 5 -1 3
-@4_1_784_155
-AATGCATGCTTCGAATGGCATTCTCTTCAATCACGA
-+4_1_784_155
-40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 31 40 40 40 40 40
-@4_1_595_150
-AAAGACGTGGCCAGATGGGTGGCCAAGTGCCCGACT
-+4_1_595_150
-40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 40 40 40 40 40 40 40 20 40 40 40 40 40 14 40 40
-';
-
- my $exam_sol = '
-@SLXA-B3_649_FC8437_R1_1_1_610_79
-GATGTGCAATACCTTTGTAGAGGAA
-+SLXA-B3_649_FC8437_R1_1_1_610_79
-YYYYYYYYYYYYYYYYYYWYWYYSU
-@SLXA-B3_649_FC8437_R1_1_1_397_389
-GGTTTGAGAAAGAGAAATGAGATAA
-+SLXA-B3_649_FC8437_R1_1_1_397_389
-YYYYYYYYYWYYYYWWYYYWYWYWW
-@SLXA-B3_649_FC8437_R1_1_1_850_123
-GAGGGTGTTGATCATGATGATGGCG
-+SLXA-B3_649_FC8437_R1_1_1_850_123
-YYYYYYYYYYYYYWYYWYYSYYYSY
-@SLXA-B3_649_FC8437_R1_1_1_362_549
-GGAAACAAAGTTTTTCTCAACATAG
-+SLXA-B3_649_FC8437_R1_1_1_362_549
-YYYYYYYYYYYYYYYYYYWWWWYWY
-@SLXA-B3_649_FC8437_R1_1_1_183_714
-GTATTATTTAATGGCATACACTCAA
-+SLXA-B3_649_FC8437_R1_1_1_183_714
-YYYYYYYYYYWYYYYWYWWUWWWQQ
-';
-
- print qq(
-solexa
-======
-$exam_sol
-scarf
-=====
-$exam_scarf
-fqint
-=====
-$exam_fqint
-);
-}
diff --git a/external/gatb-minia-pipeline/sspace/tools/qseq2fasta.pl b/external/gatb-minia-pipeline/sspace/tools/qseq2fasta.pl
deleted file mode 100755
index cb37f5ccbd07ab17553d42bf1a97be1c329a1e52..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/qseq2fasta.pl
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-
-if($#ARGV<0){
- die "Usage: $0 <file>\n";
-}
-
-open(IN,$ARGV[0]) || die "Can't open $ARGV[0] for reading --fatal.\n";
-my $fasta = $ARGV[0] . ".fa";
-open(OUT,">$fasta") || die "Can't open $fasta for writing --fatal.\n";
-
-while (<IN>) {
- chomp;
- my @parts = split(/\s+/);
- my $concat = ">$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]";
- print OUT "$concat\n";
- print OUT "$parts[8]\n";
-}
-
-close IN;
-close OUT;
-
-exit;
diff --git a/external/gatb-minia-pipeline/sspace/tools/qseq2fastq.pl b/external/gatb-minia-pipeline/sspace/tools/qseq2fastq.pl
deleted file mode 100755
index 568f2e4f5dc24039cc692ccd1d217f8cb2182eef..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/qseq2fastq.pl
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/perl
-
-use warnings;
-use strict;
-
-if($#ARGV<0){
- die "Usage: $0 <file>\n";
-}
-
-open(IN,$ARGV[0]) || die "Can't open $ARGV[0] for reading --fatal.\n";
-
-while (<IN>) {
- chomp;
- my @parts = split /\t/;
- print "@";
- print "$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
- print "$parts[8]\n";
- print "+\n";
- print "$parts[9]\n";
-}
-
-close IN;
diff --git a/external/gatb-minia-pipeline/sspace/tools/sam_bam2tab.pl b/external/gatb-minia-pipeline/sspace/tools/sam_bam2tab.pl
deleted file mode 100755
index 3f48cac3dad1ff8539c30571db5d81fce5633564..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/sspace/tools/sam_bam2tab.pl
+++ /dev/null
@@ -1,99 +0,0 @@
-########################################################################
-#Marten Boetzer BaseClear B.v. 26-07-2011 #
-#SSPACE perl sam_bam2Tab.pl #
-#This script; #
-# -converts a .sam file to a tab file containing; #
-# -contig of read 1 #
-# -start position of read 1 #
-# -end position of read 1 #
-# -contig of read 2 #
-# -start position of read 2 #
-# -end position of read 2 #
-# #
-# -Sam/Bam file should contain a read pair at consecutive #
-# lines where the first line contains the first read and #
-# second line the second read #
-# In order to have such a file, sort the sam file #
-# before using this script with SAMTools command: #
-# samtools view -uS <input.sam> | samtools sort -n - <input.sorted> #
-# #
-# -This script requires samtools to be installed #
-# #
-# -Bam files should end with .bam extension #
-# #
-#INPUT: #
-# perl sam_bam2Tab.pl <samfile> <postfixread1> <postfixread2 #
-# #
-# example: #
-# perl sam_bam2Tab.pl input.sorted.bam /1 /2 out.tab #
-# or #
-# perl sam_bam2Tab.pl input.sorted.sam /1 /2 out.tab #
-# #
-# This means that the first read is ending with /1 while the #
-# second read ends with /2 #
- #
-#OUTPUT: #
-# Output of this script is saved into #
-########################################################################
-
-my $infile = $ARGV[0];
-my $postfix1 = $ARGV[1];
-my $postfix2 = $ARGV[2];
-my $outfile = $ARGV[3];
-die "length of postfix1 ($postfix1) has not same length of postfix2 ($postfix2). Exiting...\n" if(length($postfix1) != length($postfix2));
-
-my $bam=($infile =~ /.bam$/)? 1:0;
-
-if($bam){
- open(SAM, "samtools view $infile |") or die "Can't open $infile for reading -- fatal\n";
-}else{
- open(SAM, "$infile") || die "Can't open $infile for reading -- fatal\n";
-}
-open(OUT, ">$outfile") || die "Can't open $outfile for writing -- fatal\n";
-
-my $step = 100000;
-my ($ct, $diffct, $read, $prevread, $prevline, $line);
-while($line = <SAM>){
- next if($line =~ /^@/);
- ($read, undef, $chrom) = split("\t", $line);
- next if($chrom eq "*");
- if($read !~ /$postfix1$/ && $read !~ /$postfix2$/){
- warn("read $read had no suffix '$postfix1' or '$postfix2', please insert a correct suffix (e.g. '/1' and '/2')\n");
- }
- $read = substr($read,0,-(length($postfix1)));
- if($prevread eq $read){
- $pair_found++;
- my ($line1, $line2) = ($prevline,$line);
- if($prevread =~ /$postfix2$/){
- $line1 = $line;
- $line2 = $prevline;
- }
- my @arr1 = split("\t", $line1);
- my @arr2 = split("\t", $line2);
-
- my ($tig1,$start1,$end1, $tig2,$start2,$end2) = ($arr1[2], $arr1[3], ($arr1[3]+length($arr1[9])), $arr2[2],$arr2[3],($arr2[3]+length($arr2[9])));
-
- if ($arr1[1] & 16) {
- $end1 = $start1;
- $start1 = $start1 + length($arr1[9]);
- }
- if ($arr2[1] & 16) {
- $end2 = $start2;
- $start2 = $start2 + length($arr2[9]);
- }
- print OUT "$tig1\t$start1\t$end1\t$tig2\t$start2\t$end2\n";
- }
- $prevread = $read;
- $prevline = $line;
- if(++$ct == $step){
- CounterPrint("reads = $ct pairs = $pair_found");
- $step = $step + 100000;
- }
-}
-CounterPrint("\n");
-
-sub CounterPrint{
- my $countingMessager = shift;
- print "\r$countingMessager";
- $|++;
-}
\ No newline at end of file
diff --git a/external/gatb-minia-pipeline/test/small_test_reads.fa.gz b/external/gatb-minia-pipeline/test/small_test_reads.fa.gz
deleted file mode 100644
index 8041c0c5f6e6d3215fd5b51003c5e9ba37ed09bc..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/test/small_test_reads.fa.gz and /dev/null differ
diff --git a/external/gatb-minia-pipeline/tools/__init__.py b/external/gatb-minia-pipeline/tools/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/external/gatb-minia-pipeline/tools/__init__.pyc b/external/gatb-minia-pipeline/tools/__init__.pyc
deleted file mode 100644
index 9f6319cf3265120a991d6fbe5cc1533f4f244455..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/tools/__init__.pyc and /dev/null differ
diff --git a/external/gatb-minia-pipeline/tools/estimate-insert-sizes b/external/gatb-minia-pipeline/tools/estimate-insert-sizes
deleted file mode 100755
index b743e91da0e58c14fda195ed076df78f4f2bba46..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/tools/estimate-insert-sizes
+++ /dev/null
@@ -1,114 +0,0 @@
-#!/usr/bin/env python
-doc = """
-Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to.
-Author: Rayan Chikhi
-
-short usage: <reference> <*.fastq>
-
-example:
- estimate-insert-sizes contigs.fa readsA_1.fq readsA_2.fq readsB_1.fq readsB_2.fq
-
-or, with shell globbing:
-
- estimate-insert-sizes contigs.fa *.fq
-
-special case, a single argument is interpreted as interleaved pairs:
-
- estimate-insert-sizes contigs.fa interleaved.fq
-"""
-
-""" technical note:
- by default, bwa will be executed with "-t X" to read X*100kbp sequences, instead of just 100kbp.
- 100kbp is not enough in my experience to detect insert sizes.
- incidentally, bwa will use X threads, even if the cpu has less cores than that.
- X can be changed by modifying this variable:
-"""
-
-nb_threads = 5
-
-# --------
-
-from glob import glob
-import subprocess
-import sys, os
-
-if len(sys.argv) < 3:
- exit(doc)
-
-reference = os.path.abspath(sys.argv[1])
-if "--RF" in sys.argv:
- is_mate_pairs = True
- sys.argv.remove("--RF")
-else:
- is_mate_pairs = False
-reads = sorted(sys.argv[2:])
-
-# add script's folder to path, to find BWA
-# no longer needed as i'm putting bwa as a prerequisite and not packaging it
-#os.environ["PATH"] += os.pathsep + os.path.dirname(os.path.realpath(__file__))
-
-try:
- subprocess.call(["bwa"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-except:
- exit("Please make sure that the `bwa` binary is in your $PATH")
-
-for read in reads:
- if not os.path.isfile(read):
- exit("Error: %s does not exist" % read)
-
-if len(reads) == 1:
- print "Assuming that %s is interleaved" % reads[0]
- reads += [""]
-
-if not os.path.isfile(reference+".sa"):
- print "Creating index file.."
- subprocess.call(["bwa", "index", reference], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-
-def parse_list(line, nb_elts):
- # specific to BWA-MEM stderr format
- return map(lambda x: int(float(x)), ' '.join(line.strip().replace(',','').split()[-nb_elts:])[1:-1].split())
-
-stats = dict()
-for read1, read2 in zip(reads[::2],reads[1::2]):
- print( "Processing: \n %s \n %s " % (read1,read2) )
- cmd = ["bwa", "mem"] + (["-p"] if read2 == "" else []) + ["-t %d" % nb_threads, reference, read1, read2]
- DEVNULL = open(os.devnull, 'wb')
- process = subprocess.Popen(cmd, stdout=DEVNULL, stderr=subprocess.PIPE)
- seen_candidate_line = False
- while True:
- line = process.stderr.readline()
- if line == '' and process.poll() != None:
- break
- if "worker" in line:
- break
- if "pestat" not in line:
- continue
- if "candidate unique pairs for" in line:
- if seen_candidate_line:
- break
- seen_candidate_line = True
- nb_pairs = parse_list(line,4)
- for i in xrange(4):
- stats[['FF', 'FR', 'RF', 'RR'][i]] = { 'nb_pairs' : nb_pairs[i] }
- if "orientation" in line:
- orientation = line.strip().split()[-1].replace('.','')
- if "mem_pestat] mean and std.dev:" in line:
- mean, stdev = parse_list(line,2)
- stats[orientation]['mean'] = mean
- stats[orientation]['stdev'] = stdev
- if orientation == 'RR':
- # stats are complete
- break
- sys.stdout.write(line)
- sys.stdout.flush()
- if process.poll() is None:
- process.terminate()
-
- if not is_mate_pairs:
- results = sorted(stats.items(), key = lambda x: x[1]['nb_pairs'], reverse=True)
- else:
- results = [("RF", stats["RF"])]
- most_likely = results[0]
- mean = most_likely[1]['mean']
- stdev = most_likely[1]['stdev']
- print "Orientation", most_likely[0], "mean", mean, "stdev", stdev
diff --git a/external/gatb-minia-pipeline/tools/hybrid_metagenome_assembly_cami2.txt b/external/gatb-minia-pipeline/tools/hybrid_metagenome_assembly_cami2.txt
deleted file mode 100644
index 369b0d78d1481cdee50b2537ccf56495254f26e7..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/tools/hybrid_metagenome_assembly_cami2.txt
+++ /dev/null
@@ -1,230 +0,0 @@
-Scripts we've used to perform hybrid assemblies for CAMI2.
-
-Input: a long_reads-only assembly and a short_reads-only assembly
-
-commands:
-
-minimap2 -x map-pb -m 25 -n 2 assembly_long_reads.fasta assembly_short_reads.fasta > mapping.paf
-python keep_included_sequences.py -p mapping.paf -f assembly_short_reads.fasta -v -o assembly_short_reads_less_80.fasta
-cat assembly_short_reads_less_80.fasta assembly_long_reads.fasta > reconciliation.fasta
-
-
-$ cat keep_included_sequences.py
-import sys
-import getopt
-
-class Unbuffered(object):
- def __init__(self, stream):
- self.stream = stream
- def write(self, data):
- self.stream.write(data)
- self.stream.flush()
- def writelines(self, datas):
- self.stream.writelines(datas)
- self.stream.flush()
- def __getattr__(self, attr):
- return getattr(self.stream, attr)
-
-"""
-PAF: a Pairwise mApping Format
-
-PAF is a text format describing the approximate mapping positions between two set of sequences. PAF is TAB-delimited with each line consisting of the following predefined fields:
-Col Type Description
-1 string Query sequence name
-2 int Query sequence length
-3 int Query start (0-based)
-4 int Query end (0-based)
-5 char Relative strand: "+" or "-"
-6 string Target sequence name
-7 int Target sequence length
-8 int Target start on original strand (0-based)
-9 int Target end on original strand (0-based)
-10 int Number of residue matches
-11 int Alignment block length
-12 int Mapping quality (0-255; 255 for missing)
-
-If PAF is generated from an alignment, column 10 equals the number of sequence matches, and column 11 equals the total number of sequence matches, mismatches, insertions and deletions in the alignment. If alignment is not available, column 10 and 11 are still required but may be highly inaccurate.
-"""
-
-
-"""
-Exemple
-k141_388924 314 103 244 + ctg4 717558 379417 379558 98 141 60 tp:A:P cm:i:7 s1:i:98 s2:i:44 dv:f:0.0342
-"""
-
-
-def usage():
- '''Usage'''
- print("-----------------------------------------------------------------------------")
- print(sys.argv[0]," : from a .paf file and the corresponding query fasta file (one line per sequence) output only sequences that are aligned")
- print("-----------------------------------------------------------------------------")
- print("usage: ",sys.argv[0])
- print(" -p paf file [mandatory]")
- print(" -f fasta file file [mandatory]")
- print(" -a minimal percentage of aligned part of the query (default 80)")
- print(" -q max qual [0-255] to consider an alignment (default 255)")
- print(" -v: reverse. Conserve only NON mapped sequences instead of mapped onces")
- print(" -o: output fasta file path (default = stdout)")
- print(" -h: help")
- print("-----------------------------------------------------------------------------")
- sys.exit(2)
-
-
-
-def store_ids_of_sequences_to_keep_several_lines(in_paf_file, min_percentage, max_qual_value):
- """ This function analyses contigs querys whose alignements are splitted among several lines.
- It takes as input a sorted paf, first sorted by query contigs ids (column 0) and then by target contig ids (column 5)
- This sorted paf can be pobtained thanks to "sort mapping.paf --key=1,1 --key=6,6 | cut -f 1-6 | uniq > sorted_mapping.paf"
- Example:
- k141_101350 408 116 203 - ctg186
- k141_101350 408 116 203 + ctg254
- k141_101350 408 2 70 - ctg254
- k141_101350 408 214 406 - ctg291
- k141_101350 408 214 406 - ctg392
- k141_101350 408 116 203 + ctg473
- k141_101350 408 116 203 - ctg488
- k141_101350 408 214 378 + ctg543
- Here contig k141_101350 maps ctg254 from 2 to 70 and from 116 to 203. We cumulate those lenghts. Note that we do not care about strand. This should be an improvement
- """
- num_lines = sum(1 for line in open(in_paf_file))
- file = open(in_paf_file)
- ids_of_sequences_to_keep =set()
- previous_contig_query=""
- previous_contig_target=""
- positive_mapped_positions=[]
- positive_cumulated_mapped_positions=0
- negative_mapped_positions=[]
- negative_cumulated_mapped_positions=0
- done=0
- while True:
- done+=1
- if done%1000==0:
- print(" ",str(round(100*done/num_lines, 2)),"%",end='\r')
- line = file.readline()
- if not line: break
- line=line.rstrip().split()
- if line[0]!=previous_contig_query or line[5]!=previous_contig_target: ### Reset the conters
- previous_contig_query=line[0]
- previous_contig_target=line[5]
-
- positive_mapped_positions=[0 for i in range(int(line[1]))] ### fill with zeros
- positive_cumulated_mapped_length=0
-
- negative_mapped_positions=[0 for i in range(int(line[1]))] ### fill with zeros
- negative_cumulated_mapped_length=0
-
- if line[4]=='+': ### Map positive mapped strand
- for i in range(int(line[2]), int(line[3])):
- if positive_mapped_positions[i]==0:
- positive_mapped_positions[i]==1
- positive_cumulated_mapped_length+=1
-
- if (positive_cumulated_mapped_length)/float(line[1])*100 >= min_percentage:# and int(line[11])<=max_qual_value:
- ids_of_sequences_to_keep.add(line[0])
-
- if line[4]=='-': ### Map negative mapped strand
- for i in range(int(line[2]), int(line[3])):
- if negative_mapped_positions[i]==0:
- negative_mapped_positions[i]==1
- negative_cumulated_mapped_length+=1
-
- if (negative_cumulated_mapped_length)/float(line[1])*100 >= min_percentage:# and int(line[11])<=max_qual_value:
- ids_of_sequences_to_keep.add(line[0])
- file.close()
- return ids_of_sequences_to_keep
-
-def store_ids_of_sequences_to_keep(in_paf_file, min_percentage, max_qual_value):
- """ has been, does not consider the possible split mapping of a query on a target contig
- use store_ids_of_sequences_to_keep_several_lines(in_paf_file, min_percentage, max_qual_value) instead
- """
- file = open(in_paf_file)
- ids_of_sequences_to_keep =set()
- for line in file:
- line=line.rstrip().split()
- # print (line)
- # print(int(line[3])-int(line[2]))
- # print((int(line[3])-int(line[2]))/float(line[1])*100)
- if (int(line[3])-int(line[2]))/float(line[1])*100 >= min_percentage:# and int(line[11])<=max_qual_value:
- ids_of_sequences_to_keep.add(line[0])
- file.close()
- return ids_of_sequences_to_keep
-
-def output_sequences_to_keep(in_fasta_file,ids_of_sequences_to_keep, out_file, reverse):
- output=0
- total=0
- file = open(in_fasta_file)
- if out_file:
- filout=open(out_file,'w')
- else:
- filout = sys.stdout
- while True:
- line1=file.readline()
- if not line1: break
- line2=file.readline()
-
- total+=1
- id_seq = line1.split()[0][1:]#>k141_666705 flag=1 multi=2.0000 len=309
- if not reverse and id_seq in ids_of_sequences_to_keep:
- filout.write (line1+line2)
- output+=1
- if reverse and id_seq not in ids_of_sequences_to_keep: # if reverse, keep only sequences that are NOT similar enough.
- filout.write (line1+line2)
- output+=1
- print("Nb sequences:",total)
- print("Nb output:",output)
- filout.close()
- file.close()
-
-
-
-def main():
- sys.stdout = Unbuffered(sys.stdout)
- try:
- opts, args = getopt.getopt(sys.argv[1:], "hvp:f:a:q:o:")
- except getopt.GetoptError as err:
- # print help information and exit:
- usage()
- sys.exit(2)
-
- # Default parameters
- in_paf_file = None
- in_fasta_file = None
- out_file = None
- reverse = False
- min_percentage=80
- max_qual_value=255
- for opt, arg in opts:
- if opt in ("-h", "--help"):
- usage()
- sys.exit()
- elif opt in ("-f"):
- in_fasta_file = arg
- elif opt in ("-p"):
- in_paf_file = arg
- elif opt in ("-q"):
- max_qual_value = int(arg)
- elif opt in ("-v"):
- reverse = True
- elif opt in ("-a"):
- min_percentage = int(arg)
- elif opt in ("-o", "--out"):
- out_file = arg
- else:
- assert False, "unhandled option"
-
- if in_paf_file==None:
- print ("-p missing")
- usage()
- sys.exit(2)
-
- if in_fasta_file==None:
- print ("-f missing")
- usage()
- sys.exit(2)
- ids_of_sequences_to_keep=store_ids_of_sequences_to_keep_several_lines(in_paf_file, min_percentage, max_qual_value)
- output_sequences_to_keep(in_fasta_file,ids_of_sequences_to_keep, out_file, reverse)
-
-if __name__ == "__main__":
- main()
-
-
diff --git a/external/gatb-minia-pipeline/tools/memused b/external/gatb-minia-pipeline/tools/memused
deleted file mode 100755
index 26658186700ee87876a9ab41c8dd29d2a71e3a28..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/tools/memused
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-# Author: Marc Garcia-Garcera
-# usage: memused [program arg1 arg2 ...]
-
-"$@" &
-pid=$!
-status=$(ps -o rss -o vsz -o pid | grep $pid)
-max=0
-while [ "${#status}" -gt "0" ];
-do
- sleep 0.1
- mem=$(ps -o rss -o vsz -o pid | grep $pid | awk '{print $1}')
- mem=$((mem/1024))
- if [ "0$mem" -gt "0$max" ] 2>/dev/null; then
- max=$mem
- fi
-status=$(ps -o rss -o vsz -o pid | grep $pid)
-done
-wait $pid
-ret=$?
-
-echo "maximal memory used: $max MB"
-
-exit $ret
diff --git a/external/gatb-minia-pipeline/tools/readfq.py b/external/gatb-minia-pipeline/tools/readfq.py
deleted file mode 100644
index 7cb3f4e4521774e73a9033258552c10d599b4220..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/tools/readfq.py
+++ /dev/null
@@ -1,46 +0,0 @@
-# https://github.com/lh3/readfq/blob/master/readfq.py
-# Unlicensed.
-# Thanks for that simple fastq parser that doesn't require installing a python package, Heng Li!
-
-def readfq(fp): # this is a generator function
- last = None # this is a buffer keeping the last unprocessed line
- while True: # mimic closure; is it a bad idea?
- if not last: # the first record or a record following a fastq
- for l in fp: # search for the start of the next record
- if type(l) is not str: l = l.decode('ascii') #python3 fix
- if l[0] in '>@': # fasta/q header line
- last = l[:-1] # save this line
- break
- if not last: break
- name, seqs, last = last[1:].partition(" ")[0], [], None
- for l in fp: # read the sequence
- if type(l) is not str: l = l.decode('ascii') # python3 fix
- if l[0] in '@+>':
- last = l[:-1]
- break
- seqs.append(l[:-1])
- if not last or last[0] != '+': # this is a fasta record
- yield name, ''.join(seqs), None # yield a fasta record
- if not last: break
- else: # this is a fastq record
- seq, leng, seqs = ''.join(seqs), 0, []
- for l in fp: # read the quality
- if type(l) is not str: l = l.decode('ascii') #python3 fix
- seqs.append(l[:-1])
- leng += len(l) - 1
- if leng >= len(seq): # have read enough quality
- last = None
- yield name, seq, ''.join(seqs); # yield a fastq record
- break
- if last: # reach EOF before reading enough quality
- yield name, seq, None # yield a fasta record instead
- break
-
-if __name__ == "__main__":
- import sys
- n, slen, qlen = 0, 0, 0
- for name, seq, qual in readfq(sys.stdin):
- n += 1
- slen += len(seq)
- qlen += qual and len(qual) or 0
- print(n, '\t', slen, '\t', qlen)
diff --git a/external/gatb-minia-pipeline/tools/readfq.pyc b/external/gatb-minia-pipeline/tools/readfq.pyc
deleted file mode 100644
index eec331ff6f446e9c74a6cac3f85f0766f987188a..0000000000000000000000000000000000000000
Binary files a/external/gatb-minia-pipeline/tools/readfq.pyc and /dev/null differ
diff --git a/external/gatb-minia-pipeline/tools/sga-deinterleave.pl b/external/gatb-minia-pipeline/tools/sga-deinterleave.pl
deleted file mode 100644
index 2ca76baa2cc724ae167fa48123586f791dc91aba..0000000000000000000000000000000000000000
--- a/external/gatb-minia-pipeline/tools/sga-deinterleave.pl
+++ /dev/null
@@ -1,73 +0,0 @@
-#! /usr/bin/perl
-# written by J. Simpson
-# from https://github.com/jts/sga/blob/master/src/bin/sga-deinterleave.pl
-#
-# sga-deinterleave.pl READS OUT1 OUT2
-#
-# Split the READS fasta/q file into two files, one for each half of a read pair
-#
-# modified by R. Chikhi to loosen header check
-use strict;
-my $inFile = $ARGV[0];
-my $out1File = $ARGV[1];
-my $out2File = $ARGV[2];
-
-die("No input file given") if($inFile eq "");
-die("No output file(s) given") if($out1File eq "" || $out2File eq "");
-
-open(OUT1, ">$out1File");
-open(OUT2, ">$out2File");
-open(IN, ($inFile =~ /\.gz$/)? "gzip -dc $inFile |" : $inFile) || die;
-
-my $last_header = "";
-
-while(my $line = <IN>)
-{
- chomp $line;
- my ($header) = $line; #split(' ', $line);
-
- my $record = "";
- if($header =~ /^>/)
- {
- # parse fasta, assume 1 line per sequence
- $record = $header . "\n" . <IN>;
- }
- elsif($header =~ /^@/)
- {
- # parse fastq
- $record = $header . "\n";
- $record .= <IN>;
- $record .= <IN>;
- $record .= <IN>;
- }
- else
- {
- next;
- }
-
- # emit record
- if(isFirstRead($header))
- {
- print OUT1 $record;
- die("Found two consecutive /1 read headers, exiting; (last header: $header)") if ($last_header eq "first");
- $last_header = "first";
- }
- else
- {
- print OUT2 $record;
- die("Found two consecutive /2 read headers, exiting; (last header: $header)") if ($last_header eq "second");
- $last_header = "second";
- }
-}
-
-close(OUT1);
-close(OUT2);
-close(IN);
-
-sub isFirstRead
-{
- my ($header) = @_;
- return 1 if($header =~ /[^\w]A([^\w]|$)|[^\w:]1([^\w]|$)/);
- return 0 if($header =~ /[^\w]B([^\w]|$)|[^\w:]2([^\w]|$)/);
- die("Cannot parse record $header");
-}
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_argument.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_argument.h
index e41faefc1b859556997974ecc93fa0c602a7f209..d6cd13ea9372a130a8b52369679a1c0911d4fb3c 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_argument.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_argument.h
@@ -767,7 +767,7 @@ inline void _checkStringRestrictions(ArgParseArgument const & me, std::string co
typedef std::vector<std::string>::const_iterator TVectorIterator;
// we only check valid values for files and string arguments, but not for prefix arguments
- if (!empty(me.validValues) && !(isInputPrefixArgument(me) || isOutputPrefixArgument(me)))
+ if (!seqan::empty(me.validValues) && !(isInputPrefixArgument(me) || isOutputPrefixArgument(me)))
{
// The file name "-" is reserved for stdin or stdout
if ((isInputFileArgument(me) || isOutputFileArgument(me)) && value == "-")
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_ctd_support.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_ctd_support.h
index 7f91846aa481f951431dc1076678d5de2ac447c7..c7eafea4f19b725e9edc2b3d9b6ad47f93164b26 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_ctd_support.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_ctd_support.h
@@ -136,7 +136,7 @@ inline std::string
_getPrefixedOptionName(ArgParseOption const & opt)
{
std::string optName = "";
- if (!empty(opt.longName))
+ if (!seqan::empty(opt.longName))
optName = "--" + opt.longName;
else
optName = "-" + opt.shortName;
@@ -151,7 +151,7 @@ _getPrefixedOptionName(ArgParseOption const & opt)
inline std::string
_getOptionName(ArgParseOption const & opt)
{
- if (!empty(opt.longName))
+ if (!seqan::empty(opt.longName))
return opt.longName;
else
return opt.shortName;
@@ -419,7 +419,7 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
// since we are talking about prefixes.
std::vector<std::string> supported_formats;
_getSupportedFormats(supported_formats, opt);
- if (empty(supported_formats) && (type=="input-prefix" || type=="output-prefix" ))
+ if (seqan::empty(supported_formats) && (type=="input-prefix" || type=="output-prefix" ))
supported_formats.push_back("*.*");
ctdfile << _indent(currentIndent)
@@ -434,9 +434,9 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
ctdfile << "type=\"" << type << "\" "
<< "description=\"" << xmlEscape(_toText(opt._helpText)) << "\" ";
- if (!empty(restrictions))
+ if (!seqan::empty(restrictions))
ctdfile << "restrictions=\"" << xmlEscape(_join(restrictions, ",")) << "\" ";
- if (!empty(supported_formats))
+ if (!seqan::empty(supported_formats))
ctdfile << "supported_formats=\"" << xmlEscape(_join(supported_formats, ",")) << "\" ";
ctdfile << "required=\"" << (isRequired(opt) ? "true" : "false") << "\" ";
@@ -507,7 +507,7 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
// since we are talking about prefixes.
std::vector<std::string> supported_formats;
_getSupportedFormats(supported_formats, arg);
- if (empty(supported_formats) && (type=="input-prefix" || type=="output-prefix" ))
+ if (seqan::empty(supported_formats) && (type=="input-prefix" || type=="output-prefix" ))
supported_formats.push_back("*.*");
@@ -516,9 +516,9 @@ writeCTD(ArgumentParser const & me, std::ostream & ctdfile)
<< (isListArgument(arg) ? " " : "value=\"\" ")
<< "type=\"" << type << "\" "
<< "description=\"" << xmlEscape(_toText(arg._helpText)) << "\" "; // it will be "" in most cases but we try
- if (!empty(restrictions))
+ if (!seqan::empty(restrictions))
ctdfile << "restrictions=\"" << xmlEscape(_join(restrictions, ",")) << "\" ";
- if (!empty(supported_formats))
+ if (!seqan::empty(supported_formats))
ctdfile << "supported_formats=\"" << xmlEscape(_join(supported_formats, ",")) << "\" ";
ctdfile << "required=\"true\" ";
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_doc.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_doc.h
index 0609655e19ca8e12ee73258d1928c6fcf35b915b..498378cca64c66dddb2767be69e8f31826176210 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_doc.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_doc.h
@@ -670,18 +670,18 @@ inline void printLongCopyright(ArgumentParser const & me)
inline void _addNumericalRestriction(std::string & text, ArgParseOption const & opt)
{
// expand min/max restrictions
- if (!empty(opt.minValue) || !empty(opt.maxValue))
+ if (!seqan::empty(opt.minValue) || !seqan::empty(opt.maxValue))
{
append(text, " In range [");
- if (!empty(opt.minValue))
+ if (!seqan::empty(opt.minValue))
append(text, opt.minValue);
else
append(text, "-inf");
append(text, "..");
- if (!empty(opt.maxValue))
+ if (!seqan::empty(opt.maxValue))
append(text, opt.maxValue);
else
append(text, "inf");
@@ -720,7 +720,7 @@ inline void _expandList(std::string & text, std::vector<std::string> const & lis
inline void _addDefaultValues(std::string & text, ArgParseOption const & opt)
{
- if (!empty(opt.defaultValue) && !isBooleanOption(opt))
+ if (!seqan::empty(opt.defaultValue) && !isBooleanOption(opt))
{
append(text, " Default: ");
_expandList(text, opt.defaultValue);
@@ -734,7 +734,7 @@ inline void _addDefaultValues(std::string & text, ArgParseOption const & opt)
inline void _addValidValuesRestrictions(std::string & text, ArgParseOption const & opt)
{
- if (!empty(opt.validValues) && !isBooleanOption(opt))
+ if (!seqan::empty(opt.validValues) && !isBooleanOption(opt))
{
if (isInputFileArgument(opt) || isOutputFileArgument(opt))
{
@@ -794,16 +794,16 @@ inline void printHelp(ArgumentParser const & me,
for (unsigned i = 0; i < length(me.optionMap); ++i)
{
ArgParseOption const & opt = me.optionMap[i];
- if (empty(opt.shortName) && empty(opt.longName)) // this is not an option but a text line
+ if (seqan::empty(opt.shortName) && seqan::empty(opt.longName)) // this is not an option but a text line
{
- if (empty(opt._helpText)) // TODO(holtgrew): Should go away in future.
+ if (seqan::empty(opt._helpText)) // TODO(holtgrew): Should go away in future.
continue; // Skip empty lines.
// Is command line parser section, maps to ToolDoc subsection.
for (unsigned j = i + 1; j < length(me.optionMap); ++j)
{
ArgParseOption const & nextopt = me.optionMap[j];
- if (empty(nextopt.shortName) && empty(nextopt.longName))
+ if (seqan::empty(nextopt.shortName) && seqan::empty(nextopt.longName))
break;
// has visible children
if (!isHidden(nextopt) && (!isAdvanced(nextopt) || showAdvancedOptions))
@@ -819,15 +819,15 @@ inline void printHelp(ArgumentParser const & me,
{
// Build list item term.
std::string term;
- if (!empty(opt.shortName))
+ if (!seqan::empty(opt.shortName))
{
term = "\\fB-";
append(term, opt.shortName);
append(term, "\\fP");
}
- if (!empty(opt.shortName) && !empty(opt.longName))
+ if (!seqan::empty(opt.shortName) && !seqan::empty(opt.longName))
append(term, ", ");
- if (!empty(opt.longName))
+ if (!seqan::empty(opt.longName))
{
append(term, "\\fB--");
append(term, opt.longName);
@@ -837,7 +837,7 @@ inline void printHelp(ArgumentParser const & me,
std::string arguments = getArgumentLabel(opt);
// Write arguments to term line -> only exception, boolean flags
- if (!empty(arguments))
+ if (!seqan::empty(arguments))
{
// Tokenize argument names.
std::istringstream iss(toCString(arguments));
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_option.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_option.h
index 064f23fed23041db6afb3d5499a879541f351564..a0f5dd69bb5b26eb8f5335a119e7d6de0e3db086 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_option.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_option.h
@@ -437,10 +437,10 @@ inline std::string getOptionName(ArgParseOption const & me)
{
std::stringstream stream;
- stream << (empty(me.shortName) ? "" : "-");
+ stream << (seqan::empty(me.shortName) ? "" : "-");
stream << me.shortName;
- stream << ((empty(me.shortName) || empty(me.longName) ? "" : ", "));
- if (!empty(me.longName))
+ stream << ((seqan::empty(me.shortName) || seqan::empty(me.longName) ? "" : ", "));
+ if (!seqan::empty(me.longName))
{
stream << "--";
stream << me.longName;
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_type_support.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_type_support.h
index 0d3b77225b756d98708c0eb97be4cf4afa9e6a15..8151305d89197817ef64900e8f0be684efbd4971 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_type_support.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/arg_parse_type_support.h
@@ -113,7 +113,7 @@ inline bool _convertArgumentValue(bool & dst, ArgParseOption const & opt, std::s
if (!isBooleanOption(opt))
return false;
- dst = !empty(src) && (src != "false");
+ dst = !seqan::empty(src) && (src != "false");
return true;
}
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/argument_parser.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/argument_parser.h
index c946c30ea6c52158cdbdabe935cbee2ec8b5796e..6ea14446336a19a90ed37469e2f8cbee8b86ec5e 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/argument_parser.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/argument_parser.h
@@ -310,9 +310,9 @@ inline void addOption(ArgumentParser & me, ArgParseOption const & opt)
// finally append the option
appendValue(me.optionMap, opt);
- if (!empty(opt.shortName))
+ if (!seqan::empty(opt.shortName))
me.shortNameMap.insert(std::make_pair(opt.shortName, length(me.optionMap) - 1));
- if (!empty(opt.longName))
+ if (!seqan::empty(opt.longName))
me.longNameMap.insert(std::make_pair(opt.longName, length(me.optionMap) - 1));
// handle the case of input and output option: add a string option --${name}-file-ext.
diff --git a/external/seqan-library-2.2.0/include/seqan/arg_parse/tool_doc.h b/external/seqan-library-2.2.0/include/seqan/arg_parse/tool_doc.h
index 2d10a00b1ae1d0e649750aeb9db872898252d890..5351a31cfc3c43b0cf961be0c051319ee6f0b2a4 100644
--- a/external/seqan-library-2.2.0/include/seqan/arg_parse/tool_doc.h
+++ b/external/seqan-library-2.2.0/include/seqan/arg_parse/tool_doc.h
@@ -548,7 +548,7 @@ public:
}
}
}
- if (!empty(tokens))
+ if (!seqan::empty(tokens))
stream << '\n';
}
diff --git a/external/seqan-library-2.2.0/include/seqan/basic/basic_tangle.h b/external/seqan-library-2.2.0/include/seqan/basic/basic_tangle.h
index 4190559ea48c3de04d84ad350e0fef3f18b818fb..7b3b5e985b93f25742947ed108c61f442da59c5b 100644
--- a/external/seqan-library-2.2.0/include/seqan/basic/basic_tangle.h
+++ b/external/seqan-library-2.2.0/include/seqan/basic/basic_tangle.h
@@ -40,7 +40,7 @@
namespace seqan {
// TODO(holtgrew): Remove this define.
-#define seqan seqan
+//#define seqan seqan
// ============================================================================
// Forwards
diff --git a/external/seqan-library-2.2.0/include/seqan/sequence/string_base.h b/external/seqan-library-2.2.0/include/seqan/sequence/string_base.h
index 3b10a6fe1b56601d61abca02128fb403e543d577..7229ce38b36e72e5daea766e361ab33197147731 100644
--- a/external/seqan-library-2.2.0/include/seqan/sequence/string_base.h
+++ b/external/seqan-library-2.2.0/include/seqan/sequence/string_base.h
@@ -1003,7 +1003,7 @@ struct AssignString_
TTarget & target,
TSource & source)
{
- if (empty(source) && empty(target))
+ if (seqan::empty(source) && empty(target))
return; // Do nothing if both source and target are empty.
if (!getObjectId(source) || !shareResources(target, source))
{
diff --git a/external/seqan-library-2.2.0/include/seqan/system/file_sync.h b/external/seqan-library-2.2.0/include/seqan/system/file_sync.h
index 39705af30528e2421b85b2eeea3e18f8fc8f1d82..d927be7ad832d92a446168543830e7dd4238aa4f 100644
--- a/external/seqan-library-2.2.0/include/seqan/system/file_sync.h
+++ b/external/seqan-library-2.2.0/include/seqan/system/file_sync.h
@@ -334,7 +334,7 @@ public:
if (empty(tmpDir))
tmpDir = SEQAN_DEFAULT_TMPDIR;
#else // #ifdef SEQAN_DEFAULT_TMPDIR
- if (empty(tmpDir))
+ if (seqan::empty(tmpDir))
tmpDir = "/tmp";
#endif // #ifdef SEQAN_DEFAULT_TMPDIR
diff --git a/out.txt b/out.txt
deleted file mode 100644
index 65fe1bcad186746408daf1e516701e1859b6eef0..0000000000000000000000000000000000000000
--- a/out.txt
+++ /dev/null
@@ -1,5588 +0,0 @@
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Bam_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Sam_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Sam_> >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Bam_]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:44,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1199:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1047:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1066:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::reserve(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1725:45: required from ‘static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; TExpand = seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1785:50: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize = int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/read_bam.h:247:11: required from ‘void seqan::readRecord(seqan::BamAlignmentRecord&, seqan::BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>&, TForwardIter&, const Bam&) [with TForwardIter = seqan::Iter<seqan::VirtualStream<char, seqan::Tag<seqan::Input_> >, seqan::StreamIterator<seqan::Tag<seqan::Input_> > >; TNameStore = seqan::StringSet<seqan::String<char, seqan::Alloc<> > >; TNameStoreCache = seqan::NameStoreCache<seqan::StringSet<seqan::String<char, seqan::Alloc<> > > >; TStorageSpec = seqan::Dependent<seqan::Tag<seqan::TagInsist_> >; seqan::Bam = seqan::Tag<seqan::Bam_>]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_file.h:231:19: required from ‘void seqan::readRecord(seqan::BamAlignmentRecord&, seqan::BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>&, TForwardIter&, const seqan::TagSelector<TTagList>&) [with TForwardIter = seqan::Iter<seqan::VirtualStream<char, seqan::Tag<seqan::Input_> >, seqan::StreamIterator<seqan::Tag<seqan::Input_> > >; TNameStore = seqan::StringSet<seqan::String<char, seqan::Alloc<> > >; TNameStoreCache = seqan::NameStoreCache<seqan::StringSet<seqan::String<char, seqan::Alloc<> > > >; TStorageSpec = seqan::Dependent<seqan::Tag<seqan::TagInsist_> >; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_file.h:241:15: required from ‘void seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_>, TSpec>&) [with TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:670:35: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1180:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1180 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:44,
- from src/ColoredDeBruijnGraph.h:8,
- from src/ColoredDeBruijnGraph.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from src/popins2.cpp:4:
-src/argument_parsing.h: In function ‘seqan::ArgumentParser::ParseResult checkInput(MergeOptions&)’:
-src/argument_parsing.h:1359:58: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
- 1359 | if (strcmp(options.filename_graph_in.c_str(), "")!=0 && strcmp(options.filename_colors_in.c_str(), "")==0 ||
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from src/popins_genotype.h:6,
- from src/popins2.cpp:12:
-src/variant_caller.h: In function ‘int initializeBam(char*, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, seqan::BamFileIn&)’:
-src/variant_caller.h:665:10: warning: ISO C++ forbids variable length array ‘baifileName’ [-Wvla]
- 665 | char baifileName[strlen(fileName) + 10];
- | ^~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString<THost, TSpec>::ModifiedString(THost_&&, typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type*) [with THost_ = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&; THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TSpec = seqan::Tag<seqan::ModReverse_>; typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type = void]’:
-src/ref_align.h:509:35: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 141 | _cargo()
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString<THost, TSpec>::ModifiedString(THost_&&, typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type*) [with THost_ = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TSpec = seqan::Tag<seqan::ModReverse_>; typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type = void]’:
-src/ref_align.h:631:38: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 141 | _cargo()
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:141:20: required from ‘seqan::ModifiedString<THost, TSpec>::ModifiedString(THost_&&, typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type*) [with THost_ = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&; THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TSpec = seqan::Tag<seqan::ModReverse_>; typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type = void]’
-src/ref_align.h:509:35: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:141:20: required from ‘seqan::ModifiedString<THost, TSpec>::ModifiedString(THost_&&, typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type*) [with THost_ = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TSpec = seqan::Tag<seqan::ModReverse_>; typename seqan::EnableIf<seqan::IsAnInnerHost<typename seqan::RemoveReference<T>::Type, typename seqan::RemoveReference<THost_>::Type> >::Type = void]’
-src/ref_align.h:631:38: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Vcf_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Vcf_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::True]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile<TFileFormat, TDirection, TSpec>::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag<seqan::Vcf_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins_genotype.h:83:47: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Bam_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::TagFastq_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFastq_>, seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins2_multik.h:38:48: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Sam_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Sam_> >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::TagFasta_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFastq_>, seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins2_multik.h:38:48: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Vcf_]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Vcf_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::True]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile<TFileFormat, TDirection, TSpec>::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag<seqan::Vcf_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins_genotype.h:83:47: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:138,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1491:22: required from ‘void seqan::goRoot(seqan::Iter<seqan::Index<TObject, TSpec>, seqan::VSTree<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexEsa<long unsigned int>& seqan::VertexEsa<long unsigned int>::operator=(const seqan::VertexEsa<long unsigned int>&)’ is deprecated [-Wdeprecated-copy]
- 1731 | it._parentDesc = value(it);
- | ~~~~~~~~~~~~~~~^~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:137,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:221:9: note: because ‘seqan::VertexEsa<long unsigned int>’ has user-provided ‘seqan::VertexEsa<TSize>::VertexEsa(const seqan::VertexEsa<TSize>&) [with TSize = long unsigned int]’
- 221 | VertexEsa(VertexEsa const &other):
- | ^~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:138,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘bool seqan::_goDownChar(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, TValue) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1963:27: required from ‘bool seqan::_goDownObject(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, const TObject&, seqan::False) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TObject = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1985:29: required from ‘bool seqan::goDown(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, const TObject&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TObject = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-src/adapter_removal.h:245:18: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1898:23: warning: implicitly-declared ‘constexpr seqan::VertexEsa<long unsigned int>& seqan::VertexEsa<long unsigned int>::operator=(const seqan::VertexEsa<long unsigned int>&)’ is deprecated [-Wdeprecated-copy]
- 1898 | value(it) = nodeDesc;
- | ~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:137,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:221:9: note: because ‘seqan::VertexEsa<long unsigned int>’ has user-provided ‘seqan::VertexEsa<TSize>::VertexEsa(const seqan::VertexEsa<TSize>&) [with TSize = long unsigned int]’
- 221 | VertexEsa(VertexEsa const &other):
- | ^~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:134,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/string_set_base.h: In instantiation of ‘void seqan::posLocalize(TResult&, const seqan::Pair<R1, R2, RPack>&, const seqan::String<TRightValue, TRightSpec>&) [with TResult = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TSpec = seqan::Alloc<>; T1 = long unsigned int; T2 = long unsigned int; TPack = seqan::Tag<seqan::Pack_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/string_set_base.h:696:16: required from ‘typename seqan::DisableIf<seqan::Is<seqan::IntegerConcept<TIntegral> >, typename seqan::InfixOnValue<const seqan::StringSet<TString, TSpec> >::Type>::Type seqan::infixWithLength(const seqan::StringSet<TString, TSpec>&, const TPosition&, TSize) [with TString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::Owner<>; TPosition = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; typename seqan::DisableIf<seqan::Is<seqan::IntegerConcept<TIntegral> >, typename seqan::InfixOnValue<const seqan::StringSet<TString, TSpec> >::Type>::Type = seqan::Segment<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1266:31: required from ‘typename seqan::InfixOnValue<const typename seqan::Fibre<TIndex, const seqan::Tag<seqan::FibreText_> >::Type>::Type seqan::representative(const seqan::Iter<TIndex, seqan::VSTree<TSpec> >&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::TopDown<>; typename seqan::InfixOnValue<const typename seqan::Fibre<TIndex, const seqan::Tag<seqan::FibreText_> >::Type>::Type = seqan::Segment<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-src/adapter_removal.h:251:37: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/string_set_base.h:595:12: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 595 | result = pos;
- | ~~~~~~~^~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Embl_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFastq_>, seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins2_multik.h:38:48: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Raw_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Raw_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFastq_>, seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Output_>; TSpec = void; TThrowExceptions = seqan::True]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile<TFileFormat, TDirection, TSpec>::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Output_>; TSpec = void]’
-src/popins2_multik.h:75:45: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1199:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1047:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1066:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::reserve(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:119:16: required from ‘seqan::String<TValue, seqan::Alloc<TSpec> >::String(const seqan::String<TValue, seqan::Alloc<TSpec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSpec = void]’
-src/adapter_removal.h:29:12: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1180:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Dna5_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1180 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Dna5_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:138,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter<TIndex, seqan::VSTree<TSpec> >&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::TopDown<>]’:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter<TIndex, seqan::VSTree<TSpec> >&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::TopDown<>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1492:14: required from ‘void seqan::goRoot(seqan::Iter<seqan::Index<TObject, TSpec>, seqan::VSTree<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexEsa<long unsigned int>& seqan::VertexEsa<long unsigned int>::operator=(const seqan::VertexEsa<long unsigned int>&)’ is deprecated [-Wdeprecated-copy]
- 2230 | value(it) = typename VertexDescriptor<TIndex>::Type(MinimalCtor());
- | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:137,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:221:9: note: because ‘seqan::VertexEsa<long unsigned int>’ has user-provided ‘seqan::VertexEsa<TSize>::VertexEsa(const seqan::VertexEsa<TSize>&) [with TSize = long unsigned int]’
- 221 | VertexEsa(VertexEsa const &other):
- | ^~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:138,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘bool seqan::_getNodeByChar(const seqan::Iter<seqan::Index<TText, seqan::IndexEsa<TSpec> >, seqan::VSTree<TSpec> >&, TValue, typename seqan::VertexDescriptor<seqan::Index<TText, seqan::IndexEsa<TSpec> > >::Type&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TIndexSpec = void; TSpec = seqan::TopDown<>; TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; typename seqan::VertexDescriptor<seqan::Index<TText, seqan::IndexEsa<TSpec> > >::Type = seqan::VertexEsa<long unsigned int>]’:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1896:27: required from ‘bool seqan::_goDownChar(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, TValue) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1963:27: required from ‘bool seqan::_goDownObject(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, const TObject&, seqan::False) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TObject = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1985:29: required from ‘bool seqan::goDown(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, const TObject&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TObject = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-src/adapter_removal.h:245:18: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1409:17: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 1409 | pos = saAt(child.i1, container(it));
- | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:138,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1420:17: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 1420 | pos = saAt(child.i1, container(it));
- | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:138,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter<seqan::Index<TText, seqan::IndexEsa<TSpec> >, seqan::VSTree<seqan::TopDown<TSpec> > >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TIndexSpec = void; TSpec = seqan::Preorder]’:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1897:25: required from ‘bool seqan::_goDownChar(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, TValue) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1963:27: required from ‘bool seqan::_goDownObject(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, const TObject&, seqan::False) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TObject = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1985:29: required from ‘bool seqan::goDown(seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >&, const TObject&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder; TObject = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-src/adapter_removal.h:245:18: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:1751:24: warning: implicitly-declared ‘constexpr seqan::VertexEsa<long unsigned int>& seqan::VertexEsa<long unsigned int>::operator=(const seqan::VertexEsa<long unsigned int>&)’ is deprecated [-Wdeprecated-copy]
- 1751 | it._parentDesc = value(it);
- | ~~~~~~~~~~~~~~~^~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:137,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:221:9: note: because ‘seqan::VertexEsa<long unsigned int>’ has user-provided ‘seqan::VertexEsa<TSize>::VertexEsa(const seqan::VertexEsa<TSize>&) [with TSize = long unsigned int]’
- 221 | VertexEsa(VertexEsa const &other):
- | ^~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::GenBank_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::TagFastq_>, seqan::TagList<seqan::Tag<seqan::TagFasta_>, seqan::TagList<seqan::Tag<seqan::Embl_>, seqan::TagList<seqan::Tag<seqan::GenBank_>, seqan::TagList<seqan::Tag<seqan::Raw_> > > > > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins2_multik.h:38:48: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value<TContext>::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag<seqan::Tristate_> >; TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value<TContext>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&, TValue2&) [with TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type seqan::value(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&]’
-./external/seqan-library-2.2.0/include/seqan/align/gaps_array.h:394:17: required from ‘typename seqan::Source<seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> > >::Type& seqan::source(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&) [with TSequence = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Source<seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> > >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-src/split_align.h:135:55: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 254 | new( (void*) & value(it) ) TNonConstValue(std::forward<TParam>(param_));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >*; TParam = const seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >*; TParam = const seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value<TContext>::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder<seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >, seqan::Tag<seqan::Tristate_> >; TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; typename seqan::Value<TContext>::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&, TValue2&) [with TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TValue2 = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type seqan::value(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&]’
-./external/seqan-library-2.2.0/include/seqan/align/gaps_array.h:394:17: required from ‘typename seqan::Source<seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> > >::Type& seqan::source(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&) [with TSequence = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; typename seqan::Source<seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> > >::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/split_align.h:163:65: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:133:7: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 133 | class ModifiedString<THost, ModView<TFunctor> >
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:100:7: note: synthesized method ‘seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >::ModifiedString(const seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >&)’ first required here
- 100 | class ModifiedString
- | ^~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >::ModifiedString(const seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&)’ first required here
- 254 | new( (void*) & value(it) ) TNonConstValue(std::forward<TParam>(param_));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:320:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 125 | data_iterator(other_.data_iterator)
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1201:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:320:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 586 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, TIntegral) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; TIntegral = long int]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1202:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:320:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 577 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator-(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:539:58: required from ‘void seqan::_computeBandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1588:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:320:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 647 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) - right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1199:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1047:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1066:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::reserve(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:119:16: required from ‘seqan::String<TValue, seqan::Alloc<TSpec> >::String(const seqan::String<TValue, seqan::Alloc<TSpec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5Q_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/seq_io/sequence_file.h:133:8: required from ‘seqan::FormattedFile<TFileFormat, TDirection, TSpec>::FormattedFile() [with TFileFormat = seqan::Tag<seqan::TagFastq_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-src/popins2_multik.h:36:15: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1180:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Dna5Q_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1180 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Dna5Q_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1137:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1005:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::SimpleType<unsigned char, seqan::Iupac_>; TValueTarget = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1033:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::SimpleType<unsigned char, seqan::Iupac_>; TValueTarget = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1011:31: required from ‘static void seqan::AssignString_<TExpand>::assign_(TTarget&, TSource&) [with TTarget = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; TSource = const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag<seqan::TagGenerous_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1056:42: required from ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>) [with TTargetValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TTargetSpec = seqan::Alloc<>; TSource = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:992:11: required from ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&) [with TTargetValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TTargetSpec = seqan::Alloc<>; TSource = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:170:15: required from ‘seqan::String<TValue, seqan::Alloc<TSpec> >& seqan::String<TValue, seqan::Alloc<TSpec> >::operator=(const TSource&) [with TSource = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = void]’
-src/popins_contigmap.h:107:71: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1118:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1118 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 125 | data_iterator(other_.data_iterator)
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator-(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:458:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 647 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) - right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1198:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 586 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, TIntegral) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; TIntegral = long int]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1199:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 577 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:512:53: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 125 | data_iterator(other_.data_iterator)
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type seqan::begin(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:320:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 351 | return TIterator(me, begin(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type seqan::end(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:443:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:320:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 486 | return TIterator(me, end(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:61,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container<const seqan::ModifiedIterator<THost, TSpec> >::Type seqan::container(const seqan::ModifiedIterator<THost, TSpec>&) [with THost = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; typename seqan::Container<const seqan::ModifiedIterator<THost, TSpec> >::Type = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_reverse.h:314:32: required from ‘typename seqan::Position<const seqan::ModifiedIterator<THost, seqan::Tag<seqan::ModReverse_> > >::Type seqan::position(const seqan::ModifiedIterator<THost, seqan::Tag<seqan::ModReverse_> >&) [with THost = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; typename seqan::Position<const seqan::ModifiedIterator<THost, seqan::Tag<seqan::ModReverse_> > >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1207:82: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::SplitAlignmentScout_>; TTrace = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::Tag<seqan::SplitAlignmentAlgo_>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:396:26: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TAlignConfigL&, const TAlignConfigR&, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TAlignConfigL = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >; TAlignConfigR = seqan::AlignConfig2<seqan::Tag<seqan::SplitAlignmentAlgo_>, seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >, seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsRight_> > > >; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:327:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 288 | TContainer cont(container(host(me)));
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>*; TParam = const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>*; TParam = const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value<TContext>::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::Tag<seqan::Tristate_> >; TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Value<TContext>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&, TValue2&) [with TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TValue2 = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type seqan::value(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&]’
-./external/seqan-library-2.2.0/include/seqan/align/gaps_array.h:269:34: required from ‘void seqan::_reinitArrayGaps(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&) [with TSequence = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/align/gaps_array.h:408:21: required from ‘void seqan::setSource(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, TSequence&) [with TSequence = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:433:14: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 254 | new( (void*) & value(it) ) TNonConstValue(std::forward<TParam>(param_));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type seqan::begin(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 351 | return TIterator(me, begin(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type seqan::end(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:443:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 486 | return TIterator(me, end(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >*; TParam = const seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >*; TParam = const seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value<TContext>::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder<seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >, seqan::Tag<seqan::Tristate_> >; TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; typename seqan::Value<TContext>::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&, TValue2&) [with TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TValue2 = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type seqan::value(seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> >&) [with TValue = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&]’
-./external/seqan-library-2.2.0/include/seqan/align/gaps_array.h:269:34: required from ‘void seqan::_reinitArrayGaps(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&) [with TSequence = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/gaps_array.h:408:21: required from ‘void seqan::setSource(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, TSequence&) [with TSequence = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:434:14: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:512:53: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:133:7: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 133 | class ModifiedString<THost, ModView<TFunctor> >
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:100:7: note: synthesized method ‘seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >::ModifiedString(const seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >&)’ first required here
- 100 | class ModifiedString
- | ^~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >::ModifiedString(const seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >&)’ first required here
- 254 | new( (void*) & value(it) ) TNonConstValue(std::forward<TParam>(param_));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:61,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container<const seqan::ModifiedIterator<THost, TSpec> >::Type seqan::container(const seqan::ModifiedIterator<THost, TSpec>&) [with THost = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; typename seqan::Container<const seqan::ModifiedIterator<THost, TSpec> >::Type = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_reverse.h:314:32: required from ‘typename seqan::Position<const seqan::ModifiedIterator<THost, seqan::Tag<seqan::ModReverse_> > >::Type seqan::position(const seqan::ModifiedIterator<THost, seqan::Tag<seqan::ModReverse_> >&) [with THost = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; typename seqan::Position<const seqan::ModifiedIterator<THost, seqan::Tag<seqan::ModReverse_> > >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1207:82: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:512:53: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 288 | TContainer cont(container(host(me)));
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:61,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type seqan::container(seqan::ModifiedIterator<THost, TSpec>&) [with THost = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h:278:30: required from ‘typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type seqan::container(seqan::ModifiedIterator<THost, TSpec>&) [with THost = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TSpec = seqan::Tag<seqan::ModReverse_>; typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:373:72: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSeqHValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSeqVValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSeqVIterator = seqan::ModifiedIterator<seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TColumnDescriptor = seqan::MetaColumnDescriptor<seqan::Tag<seqan::DPInitialColumn_>, seqan::Tag<seqan::FullColumn_> >; TDPProfile = seqan::DPProfile_<seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >, seqan::Tag<seqan::AffineGaps_>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:447:18: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:327:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 278 | TContainer cont(container(host(me)));
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1199:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1047:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1066:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::reserve(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:119:16: required from ‘seqan::String<TValue, seqan::Alloc<TSpec> >::String(const seqan::String<TValue, seqan::Alloc<TSpec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = void]’
-src/adapter_removal.h:88:15: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1180:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1180 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 125 | data_iterator(other_.data_iterator)
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1201:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 586 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, TIntegral) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; TIntegral = long int]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1202:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 577 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator-(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:539:58: required from ‘void seqan::_computeBandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1588:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 647 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) - right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator-(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:458:58: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-src/ref_align.h:495:53: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:61,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type seqan::container(seqan::ModifiedIterator<THost, TSpec>&) [with THost = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h:278:30: required from ‘typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type seqan::container(seqan::ModifiedIterator<THost, TSpec>&) [with THost = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TSpec = seqan::Tag<seqan::ModReverse_>; typename seqan::Container<seqan::ModifiedIterator<THost, TSpec> >::Type = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:373:72: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSeqHValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSeqVValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSeqVIterator = seqan::ModifiedIterator<seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TColumnDescriptor = seqan::MetaColumnDescriptor<seqan::Tag<seqan::DPInitialColumn_>, seqan::Tag<seqan::FullColumn_> >; TDPProfile = seqan::DPProfile_<seqan::LocalAlignment_<>, seqan::Tag<seqan::AffineGaps_>, seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:447:18: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:512:53: required from here
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 278 | TContainer cont(container(host(me)));
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TFunctor = seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> >; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type seqan::end(T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type seqan::end(seqan::ModifiedString<THost, TSpec>&, seqan::Tag<TExpand>) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type seqan::begin(const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >&, seqan::Tag<TSpec>) [with THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type = seqan::ModifiedIterator<seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:327:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 478 | return TIterator(me, end(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type>::Type seqan::begin(T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type>::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:619:22: required from ‘typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type seqan::begin(seqan::ModifiedString<THost, TSpec>&, seqan::Tag<TExpand>) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_reverse.h:503:103: required from ‘typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type seqan::end(const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >&, seqan::Tag<TSpec>) [with THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type = seqan::ModifiedIterator<seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:443:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SplitAlignmentScout_> >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::SplitAlignmentScout_> >; TSequenceH = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::SplitAlignment_<seqan::FreeEndGaps_<seqan::False, seqan::True, seqan::True, seqan::True> >; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::CompleteTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:491:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TGapModel&) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>; TGapModel = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align_split/align_split_interface.h:520:35: required from ‘auto seqan::_splitAlignmentImpl(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, seqan::Gaps<TContigSeqR>&, seqan::Gaps<TReadSeqR>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TContigSeqL = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqL = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TContigSeqR = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TReadSeqR = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TTop = false; bool TRight = true; bool TLeft = true; bool TBottom = true; TConfigSpec = seqan::Tag<seqan::Default_>]’
-src/split_align.h:202:42: required from ‘bool alignRead(std::pair<unsigned int, unsigned int>&, seqan::Dna5String, TContigSeq&, TRefSeq&, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:283:22: required from ‘bool splitAlignReads(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TContigSeq&, TRefSeq&, Location&, double, unsigned int) [with TContigSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/split_align.h:327:31: required from ‘bool loadContigAndSplitAlign(std::map<std::pair<unsigned int, unsigned int>, unsigned int>&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, TRefSeq&, seqan::Dna5String&, Location&, double, unsigned int) [with TRefSeq = seqan::ModifiedString<seqan::ModifiedString<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >; seqan::Dna5String = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
-src/split_align.h:457:129: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 343 | return TIterator(me, begin(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:24: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 125 | data_iterator(other_.data_iterator)
- | ^
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1201:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 586 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, TIntegral) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; TIntegral = long int]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1202:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 577 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) + right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator-(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’:
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:539:58: required from ‘void seqan::_computeBandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1588:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 647 | return Iter<TContainer, AdaptorIterator<TIterator, TSpec> >(container(left), hostIterator(left) - right);
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type seqan::begin(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 351 | return TIterator(me, begin(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type seqan::end(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:443:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; TGapModel = seqan::Tag<seqan::LinearGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 486 | return TIterator(me, end(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type seqan::end(T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type seqan::end(seqan::ModifiedString<THost, TSpec>&, seqan::Tag<TExpand>) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type seqan::begin(const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >&, seqan::Tag<TSpec>) [with THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type = seqan::ModifiedIterator<seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:512:53: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 478 | return TIterator(me, end(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator<TObject, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type>::Type seqan::begin(T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<T, const seqan::Tag<TSpec> >::Type>::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_string.h:619:22: required from ‘typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type seqan::begin(seqan::ModifiedString<THost, TSpec>&, seqan::Tag<TExpand>) [with THost = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<seqan::ModifiedString<THost, TSpec>, const seqan::Tag<TExpand> >::Type = seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_reverse.h:503:103: required from ‘typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type seqan::end(const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >&, seqan::Tag<TSpec>) [with THost = seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator<const seqan::ModifiedString<THost, seqan::Tag<seqan::ModReverse_> >, const seqan::Tag<TSpec> >::Type = seqan::ModifiedIterator<seqan::ModifiedIterator<seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Dna5_>*, seqan::Tag<seqan::Default_> > >, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:443:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::LocalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::AffineGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > > >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::LocalAlignment_<>; TGapCosts = seqan::Tag<seqan::AffineGaps_>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::AffineGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOff_>; TAlignmentAlgorithm = seqan::LocalAlignment_<>; TTraceFlag = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::AffineGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&, const TGapModel&) [with TTrace = seqan::String<seqan::TraceSegment_<long unsigned int, long unsigned int>, seqan::Alloc<> >; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::LocalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOff_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn<seqan::TracebackConfig_<seqan::Tag<seqan::SingleTrace_>, seqan::Tag<seqan::GapsLeft_> > >; TGapModel = seqan::Tag<seqan::AffineGaps_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:212:45: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&, const TTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TTag = seqan::Tag<seqan::AffineGaps_>]’
-./external/seqan-library-2.2.0/include/seqan/align/local_alignment_unbanded.h:226:31: required from ‘TScoreValue seqan::localAlignment(seqan::Gaps<TSequence, TSpec>&, seqan::Gaps<TSequenceV, TGapsSpecV>&, const seqan::Score<TScoreValue2, TScoreSpec>&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag<seqan::ArrayGaps_>; TSequenceV = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >; TGapsSpecV = seqan::Tag<seqan::ArrayGaps_>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/ref_align.h:438:31: required from ‘bool align(seqan::Gaps<TSequence, seqan::Tag<seqan::ArrayGaps_> >&, seqan::Gaps<TSeqB>&, TSeqA&, TSeqB&) [with TSeqA = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSeqB = seqan::ModifiedString<seqan::ModifiedString<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::ModView<seqan::FunctorComplement<seqan::SimpleType<unsigned char, seqan::Dna5_> > > >, seqan::Tag<seqan::ModReverse_> >]’
-src/ref_align.h:512:53: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 343 | return TIterator(me, begin(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:97,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::SuffixSegment>& seqan::Segment<THost_, seqan::SuffixSegment>::operator=(const seqan::Segment<THost_, seqan::SuffixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’
- 129 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SuffixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1227:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:855:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSource1 = seqan::SimpleType<unsigned char, seqan::Dna5_>*; TSource2 = seqan::SimpleType<unsigned char, seqan::Dna5_>*]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1245:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const seqan::True&) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; size_t = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1266:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; size_t = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:771:28: required from ‘static typename seqan::Size<T>::Type seqan::ClearSpaceExpandStringBase_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TExpand = seqan::Tag<seqan::TagGenerous_>; typename seqan::Size<T>::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:909:62: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::_clearSpace(seqan::String<TValue, TSpec>&, TSize, TPosition, TPosition, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TSpec = seqan::Alloc<>; TSize = long unsigned int; TPosition = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1237:67: required from ‘static void seqan::AppendString_<TExpand>::append_(TTarget&, TSource&) [with TTarget = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSource = const char; TExpand = seqan::Tag<seqan::TagGenerous_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1287:42: required from ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>) [with TTargetValue = seqan::SimpleType<unsigned char, seqan::Dna5_>; TTargetSpec = seqan::Alloc<>; TSource = char; TExpand = seqan::TagGenerous_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:903:11: required from ‘void seqan::append(TTarget&&, const TSource&) [with TTarget = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >&; TSource = char]’
-src/variant_caller.h:584:51: required from ‘int variantCallRegion(seqan::VcfRecord&, seqan::VcfFileIn&, seqan::FaiIndex&, seqan::FaiIndex&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, seqan::BamFileIn&, seqan::BamIndex<seqan::Tag<seqan::Bai_> >&, seqan::BamFileIn&, TOptions&, std::vector<double>&) [with TOptions = GenotypingOptions; seqan::VcfFileIn = seqan::FormattedFile<seqan::Tag<seqan::Vcf_>, seqan::Tag<seqan::Input_> >; seqan::BamFileIn = seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_> >]’
-src/popins_genotype.h:158:122: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1209:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Dna5_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1209 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Dna5_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveBackwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1227:30: required from ‘void seqan::arrayMoveBackward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:855:26: required from ‘void seqan::arrayMove(TSource1, TSource2, TTarget) [with TTarget = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSource1 = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSource2 = seqan::SimpleType<unsigned char, seqan::Iupac_>*]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1245:14: required from ‘void seqan::_arrayClearSpacePointer(TValue*, size_t, size_t, size_t, const seqan::True&) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; size_t = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1266:28: required from ‘void seqan::arrayClearSpace(TValue*, size_t, size_t, size_t) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; size_t = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:771:28: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1429:67: required from ‘static void seqan::ReplaceString_<TExpand>::replace_(TTarget&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, TSource&) [with TTarget = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; TSource = const char*; TExpand = seqan::Tag<seqan::TagGenerous_>; typename seqan::Size<T>::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1507:44: required from ‘void seqan::replace(seqan::String<TValue, TSpec>&, TPositionBegin, TPositionEnd, const TSourceValue*, seqan::Tag<TUsage>) [with TTargetValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TTargetSpec = seqan::Alloc<>; TPositionBegin = int; TPositionEnd = long unsigned int; TSourceValue = char; TExpand = seqan::TagGenerous_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:1040:12: required from ‘void seqan::replace(TTarget&&, TPositionBegin, TPositionEnd, const TSource&) [with TTarget = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >&; TPositionBegin = int; TPositionEnd = long unsigned int; TSource = char [1]]’
-src/adapter_removal.h:389:20: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1209:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1209 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type seqan::begin(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf<seqan::Is<seqan::StlContainerConcept<typename seqan::RemoveReference<T>::Type> >, typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type>::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:442:41: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 351 | return TIterator(me, begin(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:94,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator<const T, const seqan::Tag<seqan::Rooted_> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >; seqan::Rooted = const seqan::Tag<seqan::Rooted_>]’:
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type seqan::end(const T&, seqan::Tag<TSpec>) [with T = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator<const T, const seqan::Tag<TSpec> >::Type = seqan::Iter<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator<seqan::SimpleType<unsigned char, seqan::Iupac_>*, seqan::Tag<seqan::Default_> > >]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:443:37: required from ‘void seqan::_computeUnbandedAlignment(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const seqan::DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1584:34: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 486 | return TIterator(me, end(me, Standard()));
- | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_iterator.h:80,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:86,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
- 116 | Iter(typename Parameter_<TContainer>::Type container_, TIterator it_)
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1201:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:417:33: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>; TAlgoTag = seqan::Tag<seqan::NeedlemanWunsch_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:427:45: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::assign(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:651:15: required from ‘void seqan::operator<<(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:109:21: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet<TSequence, TSpec>&, TAlgSpec) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet<TSequence, TSpec>&, const TAlgSpec&, seqan::True) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:198:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:614:26: required from ‘bool seqan::indexCreate(seqan::Index<TObject, TSpec>&, FibreSA, TSpecAlg) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag<seqan::FibreSA_>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:658:27: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:627:19: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 627 | *_cur = *src;
- | ~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >::Iter(typename seqan::Parameter_<TContainer>::Type, TIterator) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> > seqan::operator+(const seqan::Iter<TContainer, seqan::AdaptorIterator<TIterator, TSpec> >&, int) [with TContainer = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType<unsigned char, seqan::Iupac_>*; TSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1201:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_<TAlgorithm, TGapCosts, TTracebackSpec>&) [with TDPScout = seqan::DPScout_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::If<seqan::HasTerminationCriterium_<seqan::GlobalAlignment_<> >, seqan::Terminator_<>, seqan::Tag<seqan::Default_> > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<seqan::DPCell_<int, seqan::Tag<seqan::LinearGaps_> >, seqan::Tag<seqan::SparseDPMatrix_> >, seqan::Tag<seqan::DPScoreMatrix_>, seqan::Tag<seqan::NavigateColumnWise_> >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_<seqan::DPMatrix_<unsigned char, seqan::Tag<seqan::FullDPMatrix_> >, seqan::DPTraceMatrix<seqan::Tag<seqan::TracebackOff_> >, seqan::Tag<seqan::NavigateColumnWise_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag<seqan::LinearGaps_>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_algorithm_impl.h:1586:32: required from ‘typename seqan::Value<TStatement>::Type seqan::_computeAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig<TBandSwitch>&, const seqan::DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag>&) [with TScoreValue = int; TGapScheme = seqan::Tag<seqan::LinearGaps_>; TTraceTarget = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TScoutState = seqan::DPScoutState_<seqan::Tag<seqan::Default_> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score<int, seqan::Tag<seqan::Simple_> >; TBandSwitch = seqan::Tag<seqan::BandOn_>; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<TStatement>::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:286:29: required from ‘typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type seqan::_setUpAndRunAlignment(seqan::DPContext<TScoreValue, TGapCosts>&, TTrace&, seqan::DPScoutState_<TDPScoutStateSpec>&, const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue2, TScoreSpec>&, const seqan::AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig>&) [with TScoreValue = int; TGapModel = seqan::Tag<seqan::LinearGaps_>; TDPScoutStateSpec = seqan::Tag<seqan::Default_>; TTrace = seqan::String<seqan::TraceSegment_<unsigned int, unsigned int> >; TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag<seqan::Simple_>; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig<seqan::Tag<seqan::BandOn_> >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::Tag<seqan::TracebackOff_>; typename seqan::Value<seqan::Score<TScoreValue2, TScoreSpec> >::Type = int]’
-./external/seqan-library-2.2.0/include/seqan/align/dp_setup.h:307:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:450:36: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, const seqan::AlignConfig<TOP, LEFT, RIGHT, BOTTOM, TACSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag<seqan::Default_>]’
-./external/seqan-library-2.2.0/include/seqan/align/global_alignment_banded.h:466:32: required from ‘TScoreValue seqan::globalAlignmentScore(const TSequenceH&, const TSequenceV&, const seqan::Score<TScoreValue, TScoreSpec>&, int, int) [with TSequenceH = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag<seqan::Simple_>]’
-src/adapter_removal.h:95:38: required from ‘bool startsWithTruSeq(TSequence&, HiSeqXAdapters) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; HiSeqXAdapters = seqan::Tag<HiSeqXAdapters_>]’
-src/adapter_removal.h:419:33: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:96,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment<THost_, seqan::InfixSegment>& seqan::Segment<THost_, seqan::InfixSegment>::operator=(const seqan::Segment<THost_, seqan::InfixSegment>&) [with THost_ = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >]’
- 143 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h: In instantiation of ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’:
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet<TSequence, TSpec>&, TAlgSpec) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet<TSequence, TSpec>&, const TAlgSpec&, seqan::True) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:198:34: required from ‘void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:614:26: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:347:15: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 347 | o1.i1 = typename Value<typename Value<TOut124>::Type, 1>::Type();
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:357:15: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 357 | o0.i1 = typename Value<typename Value<TOut0>::Type, 1>::Type();
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:361:15: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 361 | o3.i1 = typename Value<typename Value<TOut3>::Type, 1>::Type();
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:365:15: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 365 | o5.i1 = typename Value<typename Value<TOut5>::Type, 1>::Type();
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:369:15: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 369 | o6.i1 = typename Value<typename Value<TOut6>::Type, 1>::Type();
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:395:121: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 395 | /* 6 */ cp___(o6,0, *textIn); ++textIn; o6.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:398:122: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 398 | /* 5 */ cp___(o5,0,cp___(o6,1, *textIn)); ++textIn; o5.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:401:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 401 | /* 4 */ o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:405:123: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 405 | /* 3 */ cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))); ++textIn; o3.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:408:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 408 | /* 2 */ o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:412:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 412 | /* 1 */ o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:424:124: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 424 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:426:125: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 426 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:428:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 428 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:430:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 430 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:435:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 435 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:437:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 437 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:441:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 441 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:454:124: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 454 | /* 0 */ cp___(o0,0,cp___(o1,1,cp___(o2,2,cp___(o3,3, *textIn)))); ++textIn; o0.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:456:125: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 456 | /* 6 */ cp___(o0,1,cp___(o1,2,cp___(o2,3,cp___(o3,4, cp___(o6,0, *textIn))))); ++textIn; o6.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:458:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 458 | /* 5 */ cp___(o0,2,cp___(o1,3,cp___(o2,4,cp___(o3,5, cp___(o5,0,cp___(o6,1, *textIn)))))); ++textIn; o5.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:460:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 460 | /* 4 */ o0.i2[0] = o1.i2[1] = o2.i2[2] = o3.i2[2] = o4.i2[0] = o5.i2[0] = o6.i2[0] = (*nameIn4).i2; ++nameIn4; o4.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:465:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 465 | /* 3 */ cp___(o0,4,cp___(o1,5, cp___(o3,0,cp___(o4,1,cp___(o5,2,cp___(o6,3, *textIn)))))); ++textIn; o3.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:467:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 467 | /* 2 */ o0.i2[1] = o1.i2[2] = o2.i2[0] = o3.i2[0] = o4.i2[1] = o5.i2[1] = o6.i2[1] = (*nameIn2).i2; ++nameIn2; o2.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:109,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:471:126: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 471 | /* 1 */ o0.i2[2] = o1.i2[0] = o2.i2[1] = o3.i2[1] = o4.i2[2] = o5.i2[2] = o6.i2[2] = (*nameIn1).i2; ++nameIn1; o1.i1 = p; ++p;
- | ~~~~~~^~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(seqan::PairIncrementer_<TPair, TLimits>&, const TLimits2&) [with TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimits = seqan::String<long unsigned int, seqan::Alloc<> >; TLimits2 = seqan::String<long unsigned int, seqan::Alloc<> >]’:
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:382:16: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet<TSequence, TSpec>&, TAlgSpec) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet<TSequence, TSpec>&, const TAlgSpec&, seqan::True) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:857:16: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 857 | me.pos = TPair(0, 0);
- | ~~~~~~~^~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::pop(seqan::Pipe<TInput, TSpec>&, TValue&) [with TInput = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Skew7>; TSpec = seqan::Counter; TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/index/pump_separator7.h:62:16: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Skew7>, seqan::Counter>; TFunctor = seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >; TOut1 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut2 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut4 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:386:41: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet<TSequence, TSpec>&, TAlgSpec) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet<TSequence, TSpec>&, const TAlgSpec&, seqan::True) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:470:14: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 470 | Ref_ = *me;
- | ~~~~~^~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet<TSequence, TSpec>&, TAlgSpec) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TString = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet<TSequence, TSpec>&, const TAlgSpec&, seqan::True) [with TSA = seqan::String<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Alloc<> >; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:65,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, seqan::BitPacked<> >, TPair, TLimitsString> >& seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, seqan::BitPacked<> >, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:317:20: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h:578:20: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 578 | tmp.i1 = localPos;
- | ~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:324:41: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop(seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:874:13: required from ‘void seqan::Pool<TValue, TSpec>::pop(TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1148:9: required from ‘void seqan::pop(seqan::Pool<TValue, TPoolSpec>&, TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_separator7.h:62:16: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TFunctor = seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >; TOut1 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut2 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut4 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:342:37: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:751:18: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 751 | Ref_ = *cur;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type*) [with TLimitsString_ = seqan::String<long unsigned int, seqan::Alloc<> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; typename seqan::EnableIf<seqan::IsSameType<TLimitsString, TLimitsString_> >::Type = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:110,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::_copy(seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::TSkewDCStream&, const seqan::Triple<T1, T2, seqan::Tuple<T, SIZE, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T = seqan::SimpleType<unsigned char, seqan::Dna5_>; unsigned int SIZE = 6; TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::TSkewDCStream = seqan::SkewDCStream<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >; typename seqan::Value<TContext>::Type = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:405:26: required from ‘void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::insertStream(unsigned int) [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:465:13: required from ‘seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >& seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::operator++() [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >& seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:626:108: required from ‘void seqan::assign(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:651:15: required from ‘void seqan::operator<<(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:109:21: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:386:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 386 | memcpy(&dst.i.i1, &src.i1, sizeof(T1));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:76:8: note: ‘struct seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ declared here
- 76 | struct Pair<T1, T2, Pack>
- | ^~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:110,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::_copy(seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::TSkewDCStream&, const seqan::Triple<T1, T2, seqan::Tuple<T, SIZE, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T = seqan::SimpleType<unsigned char, seqan::Dna5_>; unsigned int SIZE = 4; TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::TSkewDCStream = seqan::SkewDCStream<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >; typename seqan::Value<TContext>::Type = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:423:26: required from ‘void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::insertStream(unsigned int) [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:465:13: required from ‘seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >& seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::operator++() [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >& seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:626:108: required from ‘void seqan::assign(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:651:15: required from ‘void seqan::operator<<(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:109:21: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:386:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 386 | memcpy(&dst.i.i1, &src.i1, sizeof(T1));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:76:8: note: ‘struct seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ declared here
- 76 | struct Pair<T1, T2, Pack>
- | ^~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/index.h:110,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h: In instantiation of ‘static void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::_copy(seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::TSkewDCStream&, const seqan::Triple<T1, T2, seqan::Tuple<T, SIZE, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T = seqan::SimpleType<unsigned char, seqan::Dna5_>; unsigned int SIZE = 5; TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::TSkewDCStream = seqan::SkewDCStream<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >; typename seqan::Value<TContext>::Type = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:432:26: required from ‘void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::insertStream(unsigned int) [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:465:13: required from ‘seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >& seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::operator++() [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:431:13: required from ‘seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >& seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:626:108: required from ‘void seqan::assign(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:651:15: required from ‘void seqan::operator<<(seqan::String<TValue, TSpec>&, seqan::Pipe<TInput, TSpec>&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Skew7, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:109:21: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:386:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘struct seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 386 | memcpy(&dst.i.i1, &src.i1, sizeof(T1));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:76:8: note: ‘struct seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ declared here
- 76 | struct Pair<T1, T2, Pack>
- | ^~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘const typename seqan::Value<seqan::Pipe<TInput, seqan::Namer<TCompare> > >::Type& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator*() [with TInput = seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>; typename seqan::Value<seqan::Pipe<TInput, seqan::Namer<TCompare> > >::Type = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_filter.h:124:22: required from ‘const typename seqan::Value<seqan::Pipe<TInput, seqan::Filter<TFunctor> > >::Type seqan::Pipe<TInput, seqan::Filter<TFunctor> >::operator*() const [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >; typename seqan::Value<seqan::Pipe<TInput, seqan::Filter<TFunctor> > >::Type = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:24: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:108:20: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 108 | tmp.i1 = getValueI1(*in);
- | ~~~~~~~^~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe<TInput, seqan::Namer<TCompare> >& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator++() [with TInput = seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_filter.h:129:13: required from ‘seqan::Pipe<TInput, seqan::Filter<TFunctor> >& seqan::Pipe<TInput, seqan::Filter<TFunctor> >::operator++() [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >; TFunctor = seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:328:26: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:117:22: warning: implicitly-declared ‘constexpr seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 117 | last = *in;
- | ~~~~~^~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_separator7.h:64:21: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TFunctor = seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >; TOut1 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut2 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut4 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:342:37: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_separator7.h:64:21: required from ‘void seqan::_skew7SeparateSlices(TInput&, const TFunctor&, TOut1&, TOut2&, TOut4&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TFunctor = seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >; TOut1 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut2 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut4 = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:342:37: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe<TInput, seqan::Multi<seqan::Skew7, TPair, TLimitsString> >::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TPair_ = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:294:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:937:25: required from ‘bool seqan::writeBucket(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TPageOfs&, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TPageOfs = unsigned int; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:580:31: required from ‘bool seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::_writeBucket(seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket&, unsigned int) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket = seqan::PageBucket<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:536:29: required from ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:317:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(seqan::Pipe<TInput, seqan::Namer<TCompare> >&, const ControlBeginRead&) [with TInput = seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>; seqan::ControlBeginRead = seqan::Tag<seqan::ControlBeginRead_>]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:507:23: required from ‘bool seqan::control(seqan::Pipe<TInput, TSpec>&, const TCommand&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >; TSpec = seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > >; TCommand = seqan::Tag<seqan::ControlBeginRead_>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:547:23: required from ‘bool seqan::beginRead(seqan::Pipe<TInput, TSpec>&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >; TSpec = seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1325:23: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:328:26: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:138:21: warning: implicitly-declared ‘constexpr seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 138 | me.last = *me.in;
- | ~~~~~~~~^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:139:23: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 139 | me.tmp.i1 = me.last.i1;
- | ~~~~~~~~~~^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:401:109: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:341:41: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe<TInput, seqan::Namer<TCompare> >& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator++() [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:117:22: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 117 | last = *in;
- | ~~~~~^~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:352:45: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: required from ‘seqan::Pipe<TInput, seqan::Skew7>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::setHost(seqan::PairDecrementer_<TPair, TLimits, m>&, const TLimits2&) [with TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimits = seqan::String<long unsigned int, seqan::Alloc<> >; unsigned int m = 7; TLimits2 = seqan::String<long unsigned int, seqan::Alloc<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h:516:20: required from ‘void seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, seqan::BitPacked<> >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h:592:9: required from ‘bool seqan::control(seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, TPack>, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; unsigned int m = 7; TPack = seqan::BitPacked<>; TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; seqan::ControlBeginRead = seqan::Tag<seqan::ControlBeginRead_>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:547:23: required from ‘bool seqan::beginRead(seqan::Pipe<TInput, TSpec>&) [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1325:23: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:946:16: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 946 | me.pos = TPair(0, 0);
- | ~~~~~~~^~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:65,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h: In instantiation of ‘void seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, seqan::BitPacked<> >, TPair, TLimitsString> >::fill() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h:523:13: required from ‘void seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, seqan::BitPacked<> >, TPair, TLimitsString> >::prepare() [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; unsigned int m = 7; TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h:592:9: required from ‘bool seqan::control(seqan::Pipe<TInput, seqan::Multi<seqan::Sampler<m, TPack>, TPair, TLimitsString> >&, const ControlBeginRead&) [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; unsigned int m = 7; TPack = seqan::BitPacked<>; TPair = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >; seqan::ControlBeginRead = seqan::Tag<seqan::ControlBeginRead_>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:547:23: required from ‘bool seqan::beginRead(seqan::Pipe<TInput, TSpec>&) [with TInput = seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >; TSpec = seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1325:23: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::ConcatenatorManyToOne<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::CasterReinterpret> >, seqan::Multi<seqan::Sampler<7, seqan::BitPacked<> >, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_sampler.h:536:20: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 536 | tmp.i1 = localPos;
- | ~~~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:937:25: required from ‘bool seqan::writeBucket(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TPageOfs&, TFile&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TPageOfs = unsigned int; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:580:31: required from ‘bool seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::_writeBucket(seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket&, unsigned int) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket = seqan::PageBucket<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:536:29: required from ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(seqan::Pipe<TInput, seqan::Namer<TCompare> >&, const ControlBeginRead&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>; seqan::ControlBeginRead = seqan::Tag<seqan::ControlBeginRead_>]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:547:23: required from ‘bool seqan::beginRead(seqan::Pipe<TInput, TSpec>&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TSpec = seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1325:23: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:345:26: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:138:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 138 | me.last = *me.in;
- | ~~~~~~~~^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew7>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:312:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:937:25: required from ‘bool seqan::writeBucket(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TPageOfs&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TPageOfs = unsigned int; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:580:31: required from ‘bool seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::_writeBucket(seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket&, unsigned int) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket = seqan::PageBucket<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:536:29: required from ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Sampler<7, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Sampler<7, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Sampler<7, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:335:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender7.h:148:104: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:362:29: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:247:41: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: required from ‘seqan::Pipe<TInput, seqan::Skew3>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘seqan::Pipe<TInput, seqan::Namer<TCompare> >& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator++() [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: required from ‘seqan::Pipe<TInput, seqan::Skew3>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:117:22: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 117 | last = *in;
- | ~~~~~^~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool<TValue, TSpec>::~Pool() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:259:45: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: required from ‘seqan::Pipe<TInput, seqan::Skew3>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 534 | *cb->cur = pool.undefinedValue;
- | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut12 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: required from ‘seqan::Pipe<TInput, seqan::Skew3>::Pipe(TInput&) [with TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7Multi<TLimitsString> >::insertStream(unsigned int) [with TInput0 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 4, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 5, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TLimitsString = seqan::String<long unsigned int, seqan::Alloc<> >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncReadAt(seqan::File<seqan::Async<TSpec> >&, TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:627:38: required from ‘bool seqan::readPage(int, seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, TFile&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:873:28: required from ‘bool seqan::readPage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:370:32: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::_read(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:323:13: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:882:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 882 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:64,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h: In instantiation of ‘bool seqan::control(seqan::Pipe<TInput, seqan::Namer<TCompare> >&, const ControlBeginRead&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>; seqan::ControlBeginRead = seqan::Tag<seqan::ControlBeginRead_>]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:547:23: required from ‘bool seqan::beginRead(seqan::Pipe<TInput, TSpec>&) [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TSpec = seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1325:23: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:251:26: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_namer.h:138:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 138 | me.last = *me.in;
- | ~~~~~~~~^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut12 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut12 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe<TInput, seqan::Skew3>::process(TInput_&) [with TInput_ = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:218:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:937:25: required from ‘bool seqan::writeBucket(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TPageOfs&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TPageOfs = unsigned int; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:580:31: required from ‘bool seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::_writeBucket(seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket&, unsigned int) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::TPageBucket = seqan::PageBucket<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:536:29: required from ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:633:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:902:17: required from ‘bool seqan::Pool<TValue, TSpec>::endWrite() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:786:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_filter.h:129:13: required from ‘seqan::Pipe<TInput, seqan::Filter<TFunctor> >& seqan::Pipe<TInput, seqan::Filter<TFunctor> >::operator++() [with TInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TFunctor = seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>]’
-./external/seqan-library-2.2.0/include/seqan/index/index_sa_lss.h:415:38: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:56,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >; seqan::Handler<TBufferHandler, seqan::AdapterSpec>::TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Sampler<3> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Sampler<3> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: required from ‘bool seqan::operator<<(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Sampler<3> >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:241:20: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 762 | *cur = Val_;
- | ~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pump_extender3.h:86:38: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >; TNameInput = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TOut12 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:269:29: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::push(const TValue&) [with TBufferHandler = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; seqan::Handler<TBufferHandler, seqan::MapperMemAdapter>::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:622:30: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 311 | buffer[pool.handlerArgs(Val_)] = Val_;
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:623:29: required from ‘void seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::push(const TValue&) [with THandler1 = seqan::Handler<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::MapperAsyncWriter>; seqan::Handler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:879:13: required from ‘void seqan::Pool<TValue, TSpec>::push(const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1165:9: required from ‘void seqan::push(seqan::Pool<TValue, TPoolSpec>&, const TValue&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1327:17: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: required from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1374:22: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 517 | *cb.cur = item;
- | ~~~~~~~~^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe<seqan::Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5>, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 3, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput3 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput5 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 4, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 1, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput6 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 5, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, 2, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput124 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 3, void>; T3 = seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncReadAt(seqan::File<seqan::Async<TSpec> >&, TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:627:38: required from ‘bool seqan::readPage(int, seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:873:28: required from ‘bool seqan::readPage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:370:32: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::_read(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:323:13: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 6, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:882:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 882 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13: required from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1367:42: [ skipping 14 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >& seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:55,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/pair_packed.h:91:5: note: because ‘seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >::Pair(const seqan::Pair<T1, T2, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = long unsigned int]’
- 91 | Pair(Pair const &_p) : i1(_p.i1), i2(_p.i2) {}
- | ^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncWriteAt(seqan::File<seqan::Async<TSpec> >&, const TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:750:40: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, int, TFile&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:883:29: required from ‘bool seqan::writePage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:500:33: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::_write(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame&) [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:454:13: required from ‘void seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::WriteFileSpec_> >::end() [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:561:29: required from ‘void seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::end() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::WriteFileSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:773:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:930:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 930 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer<TValue>& seqan::processBuffer(seqan::Buffer<TValue, seqan::PageFrame<typename TConfig::File, seqan::Dynamic> >&, seqan::BufferHandler<seqan::Pool<TValue, seqan::MapperSpec<TConfig> >, seqan::Tag<seqan::ReadFileSpec_> >&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TConfig = seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > >; typename TConfig::File = seqan::File<seqan::Async<> >]’:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: required from ‘void seqan::Handler<TBufferHandler, seqan::AdapterSpec>::pop() [with TBufferHandler = seqan::BufferHandler<seqan::Bundle2<seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >, seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> > >, seqan::Tag<seqan::MultiplexSpec_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:868:13: required from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe<seqan::Bundle2<TInput1, TInput2>, seqan::Merger3>& seqan::Pipe<seqan::Bundle2<TInput1, TInput2>, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput12 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’
-./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:329:13: [ skipping 16 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 202 | *refNext = *I;
- | ~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 203 | *I = *refPrev;
- | ~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/pipe.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/index.h:42,
- from src/adapter_removal.h:3,
- from src/crop_unmapped.h:7,
- from src/popins2_crop_unmapped.h:9,
- from src/popins2.cpp:5:
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >& seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >::operator=(const seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >&)’ is deprecated [-Wdeprecated-copy]
- 243 | *cur = *refPrev;
- | ~~~~~^~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_aggregate.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >’ has user-provided ‘seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >::Triple(const seqan::Triple<T1, T2, T3, seqan::Tag<seqan::Pack_> >&) [with T1 = long unsigned int; T2 = seqan::Tuple<long unsigned int, 2, void>; T3 = seqan::Tuple<long unsigned int, 2, void>]’
- 82 | inline Triple(Triple const &_p)
- | ^~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/system.h:87,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:73,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:46,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncReadAt(seqan::File<seqan::Async<TSpec> >&, TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:627:38: required from ‘bool seqan::readPage(int, seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:873:28: required from ‘bool seqan::readPage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:370:32: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::_read(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:323:13: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 3, void>, seqan::Tuple<long unsigned int, 6, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: [ skipping 16 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:882:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 882 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h: In instantiation of ‘bool seqan::asyncReadAt(seqan::File<seqan::Async<TSpec> >&, TValue*, TSize, TPos, seqan::AiocbWrapper&) [with TSpec = void; TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSize = long unsigned int; TPos = long int]’:
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:627:38: required from ‘bool seqan::readPage(int, seqan::Buffer<TValue, seqan::PageFrame<TFile, TSpec> >&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >; TSpec = seqan::Dynamic]’
-./external/seqan-library-2.2.0/include/seqan/file/file_page.h:873:28: required from ‘bool seqan::readPage(seqan::Buffer<TValue, seqan::PageFrame<TFile, seqan::Dynamic> >&, TFile&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TFile = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:370:32: required from ‘bool seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::_read(seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame&) [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TPageFrame = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::PageFrame<seqan::File<seqan::Async<> >, seqan::Dynamic> >; typename seqan::Pool<TValue, TPoolSpec>::File = seqan::File<seqan::Async<> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:323:13: required from ‘seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer& seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::next() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; seqan::BufferHandler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadFileSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:556:51: required from ‘seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::next() [with TBufferHandler1 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::MemorySpec_> >; TBufferHandler2 = seqan::BufferHandler<seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Tag<seqan::ReadFileSpec_> >; seqan::BufferHandler<seqan::Bundle2<TInput1, TInput2>, seqan::Tag<seqan::MultiplexSpec_> >::TBuffer = seqan::Buffer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Simple_> >]’
-./external/seqan-library-2.2.0/include/seqan/pipe/pipe_base.h:744:24: [ skipping 19 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_base.h:452:21: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’
-src/adapter_removal.h:241:49: required from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; typename seqan::Size<TRight>::Type = long unsigned int]’
-src/adapter_removal.h:378:43: required from ‘int removeAdapter(seqan::BamAlignmentRecord&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, seqan::Index<seqan::StringSet<TString, seqan::Owner<> > >&, unsigned int, TTag) [with TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TTag = seqan::Tag<HiSeqXAdapters_>; typename seqan::DefaultIndexSpec<seqan::StringSet<TString, seqan::Owner<> > >::Type = seqan::IndexEsa<>]’
-src/crop_unmapped.h:425:67: required from ‘int crop_unmapped(double&, seqan::Triple<seqan::String<char, seqan::Alloc<> > >&, seqan::CharString&, const CharString&, int, TAdapterTag, float) [with TAdapterTag = seqan::Tag<HiSeqXAdapters_>; seqan::CharString = seqan::String<char, seqan::Alloc<> >]’
-src/popins2_crop_unmapped.h:96:134: required from here
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:882:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct seqan::AiocbWrapper’ with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess]
- 882 | memset(&request, 0, sizeof(aiocb));
- | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-./external/seqan-library-2.2.0/include/seqan/system/file_async.h:813:8: note: ‘struct seqan::AiocbWrapper’ declared here
- 813 | struct AiocbWrapper :
- | ^~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_allocator.h:54,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::PageBucketExtended<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >, seqan::Alloc<> >; TValue = seqan::PageBucketExtended<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
- inlined from ‘typename seqan::Value<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type* seqan::_allocateStorage(seqan::String<TValue, seqan::Alloc<TSpec> >&, TSize) [with TValue = seqan::PageBucketExtended<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >; TSpec = void; TSize = long unsigned int]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:360:13,
- inlined from ‘void seqan::pop(seqan::PriorityType<TValue, TLess, seqan::PriorityHeap>&) [with TValue = seqan::PageBucketExtended<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> > >; TLess = seqan::MergeStreamComparer<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> >]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1532:28,
- inlined from ‘void seqan::Handler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadSorterSpec_> >::pop() [with TValue = seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >; TPoolSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_sorter.h:260:31,
- inlined from ‘seqan::Pipe<TInput, seqan::Namer<TCompare> >& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator++() [with TInput = seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:613:29,
- inlined from ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pipe_filter.h:129:13:
-./external/seqan-library-2.2.0/include/seqan/basic/allocator_interface.h:230:33: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
- 230 | data = (TValue *) operator new(count * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/9/bits/exception_ptr.h:40,
- from /usr/include/c++/9/exception:143,
- from /usr/include/c++/9/ios:39,
- from /usr/include/c++/9/ostream:38,
- from /usr/include/c++/9/iostream:39,
- from src/popins2.cpp:1:
-/usr/include/c++/9/new: In function ‘bool seqan::append(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::filterI1<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NCompMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::Dna5_>, 7, seqan::BitPacked<> >, seqan::Tag<seqan::Pack_> >, int> > >, seqan::Filter<seqan::_skew7GlobalSlicedMulti<seqan::Pair<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::String<long unsigned int, seqan::Alloc<> >, long unsigned int, seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> > > > >]’:
-/usr/include/c++/9/new:125:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
- 125 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_allocator.h:54,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >, seqan::Alloc<> >; TValue = seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
- inlined from ‘typename seqan::Value<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type* seqan::_allocateStorage(seqan::String<TValue, seqan::Alloc<TSpec> >&, TSize) [with TValue = seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >; TSpec = void; TSize = long unsigned int]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:360:13,
- inlined from ‘void seqan::pop(seqan::PriorityType<TValue, TLess, seqan::PriorityHeap>&) [with TValue = seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >; TLess = seqan::MergeStreamComparer<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> >]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1532:28,
- inlined from ‘void seqan::Handler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadSorterSpec_> >::pop() [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TPoolSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_sorter.h:260:31,
- inlined from ‘seqan::Pipe<TInput, seqan::Namer<TCompare> >& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator++() [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:613:29,
- inlined from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13:
-./external/seqan-library-2.2.0/include/seqan/basic/allocator_interface.h:230:33: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
- 230 | data = (TValue *) operator new(count * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/9/bits/exception_ptr.h:40,
- from /usr/include/c++/9/exception:143,
- from /usr/include/c++/9/ios:39,
- from /usr/include/c++/9/ostream:38,
- from /usr/include/c++/9/iostream:39,
- from src/popins2.cpp:1:
-/usr/include/c++/9/new: In function ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew7NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew7NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 7, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’:
-/usr/include/c++/9/new:125:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
- 125 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_allocator.h:54,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >, seqan::Alloc<> >; TValue = seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
- inlined from ‘typename seqan::Value<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type* seqan::_allocateStorage(seqan::String<TValue, seqan::Alloc<TSpec> >&, TSize) [with TValue = seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >; TSpec = void; TSize = long unsigned int]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:360:13,
- inlined from ‘void seqan::pop(seqan::PriorityType<TValue, TLess, seqan::PriorityHeap>&) [with TValue = seqan::PageBucketExtended<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> > >; TLess = seqan::MergeStreamComparer<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> >]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1532:28,
- inlined from ‘void seqan::Handler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadSorterSpec_> >::pop() [with TValue = seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >; TPoolSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_sorter.h:260:31,
- inlined from ‘seqan::Pipe<TInput, seqan::Namer<TCompare> >& seqan::Pipe<TInput, seqan::Namer<TCompare> >::operator++() [with TInput = seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TCompare = seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:613:29,
- inlined from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13:
-./external/seqan-library-2.2.0/include/seqan/basic/allocator_interface.h:230:33: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
- 230 | data = (TValue *) operator new(count * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/9/bits/exception_ptr.h:40,
- from /usr/include/c++/9/exception:143,
- from /usr/include/c++/9/ios:39,
- from /usr/include/c++/9/ostream:38,
- from /usr/include/c++/9/iostream:39,
- from src/popins2.cpp:1:
-/usr/include/c++/9/new: In function ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Namer<seqan::_skew3NComp<seqan::Pair<long unsigned int, seqan::Tuple<long unsigned int, 3, seqan::Tag<seqan::Pack_> >, seqan::Tag<seqan::Pack_> >, int> > >]’:
-/usr/include/c++/9/new:125:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
- 125 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_allocator.h:54,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::PageBucketExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> > >, seqan::Alloc<> >; TValue = seqan::PageBucketExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> > >; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
- inlined from ‘typename seqan::Value<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type* seqan::_allocateStorage(seqan::String<TValue, seqan::Alloc<TSpec> >&, TSize) [with TValue = seqan::PageBucketExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> > >; TSpec = void; TSize = long unsigned int]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:360:13,
- inlined from ‘void seqan::pop(seqan::PriorityType<TValue, TLess, seqan::PriorityHeap>&) [with TValue = seqan::PageBucketExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> > >; TLess = seqan::MergeStreamComparer<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int> >]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1532:28,
- inlined from ‘void seqan::Handler<seqan::Pool<TValue, TPoolSpec>, seqan::Tag<seqan::ReadSorterSpec_> >::pop() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TPoolSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_sorter.h:260:31,
- inlined from ‘seqan::Pool<TValue, TSpec>& seqan::Pool<TValue, TSpec>::operator++() [with TValue = seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >; TSpec = seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > >]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:613:29,
- inlined from ‘seqan::Pipe<seqan::Bundle2<TInput1, TInput2>, seqan::Merger3>& seqan::Pipe<seqan::Bundle2<TInput1, TInput2>, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::SorterSpec<seqan::SorterConfigSize<seqan::_skew3ExtendComp<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, int>, long unsigned int, seqan::File<seqan::Async<> > > > >; TInput12 = seqan::Pool<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapExtended<seqan::Triple<long unsigned int, seqan::Tuple<long unsigned int, 2, void>, seqan::Tuple<long unsigned int, 2, void>, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >]’ at ./external/seqan-library-2.2.0/include/seqan/index/pipe_merger3.h:127:17,
- inlined from ‘seqan::Pipe<TInput, seqan::Counter>& seqan::Pipe<TInput, seqan::Counter>::operator++() [with TInput = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Skew3>, seqan::Filter<seqan::_skew3UnslicerFunc<long unsigned int, long unsigned int> > >]’ at ./external/seqan-library-2.2.0/include/seqan/index/index_skew3.h:329:13,
- inlined from ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Skew3>, seqan::Filter<seqan::_skew3UnslicerFunc<long unsigned int, long unsigned int> > >, seqan::Counter>]’ at ./external/seqan-library-2.2.0/include/seqan/pipe/pool_base.h:1328:13:
-./external/seqan-library-2.2.0/include/seqan/basic/allocator_interface.h:230:33: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
- 230 | data = (TValue *) operator new(count * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/9/bits/exception_ptr.h:40,
- from /usr/include/c++/9/exception:143,
- from /usr/include/c++/9/ios:39,
- from /usr/include/c++/9/ostream:38,
- from /usr/include/c++/9/iostream:39,
- from src/popins2.cpp:1:
-/usr/include/c++/9/new: In function ‘bool seqan::assign(seqan::Pool<TValue, TPoolSpec>&, TSource&) [with TValue = seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >; TSpec = seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapLinear<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > >; TSource = seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::Pipe<seqan::Pool<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, seqan::MapperSpec<seqan::MapperConfigSize<seqan::_skew3NMapSliced<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int>, long unsigned int, seqan::File<seqan::Async<> > > > >, seqan::Filter<seqan::filterI2<seqan::Pair<long unsigned int, long unsigned int, seqan::Tag<seqan::Pack_> >, long unsigned int> > >, seqan::Skew3>, seqan::Filter<seqan::_skew3UnslicerFunc<long unsigned int, long unsigned int> > >, seqan::Counter>]’:
-/usr/include/c++/9/new:125:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
- 125 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_allocator.h:54,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::Pair<long unsigned int, long unsigned int> >; TValue = seqan::Pair<long unsigned int, long unsigned int>; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
- inlined from ‘static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::Pair<long unsigned int, long unsigned int> >; TExpand = seqan::Tag<seqan::TagGenerous_>]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:360:13,
- inlined from ‘void seqan::createChildtab(TDest&, const TLCPInput&) [with TLCPInput = seqan::String<long unsigned int, seqan::Alloc<> >; TDest = seqan::String<long unsigned int, seqan::Alloc<> >]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1785:50,
- inlined from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’ at ./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:652:23,
- inlined from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’ at ./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42,
- inlined from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::ModifiedString<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::Tag<seqan::ModReverse_> >]’ at src/adapter_removal.h:241:49:
-./external/seqan-library-2.2.0/include/seqan/basic/allocator_interface.h:230:33: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
- 230 | data = (TValue *) operator new(count * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/9/bits/exception_ptr.h:40,
- from /usr/include/c++/9/exception:143,
- from /usr/include/c++/9/ios:39,
- from /usr/include/c++/9/ostream:38,
- from /usr/include/c++/9/iostream:39,
- from src/popins2.cpp:1:
-/usr/include/c++/9/new: In function ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::ModifiedString<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::Tag<seqan::ModReverse_> >]’:
-/usr/include/c++/9/new:125:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
- 125 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_allocator.h:54,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:74,
- from ./external/seqan-library-2.2.0/include/seqan/arg_parse.h:44,
- from src/util.h:9,
- from src/argument_parsing.h:10,
- from src/popins2.cpp:4:
-In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::Pair<long unsigned int, long unsigned int> >; TValue = seqan::Pair<long unsigned int, long unsigned int>; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
- inlined from ‘static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::Pair<long unsigned int, long unsigned int> >; TExpand = seqan::Tag<seqan::TagGenerous_>]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_alloc.h:360:13,
- inlined from ‘void seqan::createChildtab(TDest&, const TLCPInput&) [with TLCPInput = seqan::String<long unsigned int, seqan::Alloc<> >; TDest = seqan::String<long unsigned int, seqan::Alloc<> >]’ at ./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1785:50,
- inlined from ‘void seqan::_indexRequireTopDownIteration(seqan::Index<TText, seqan::IndexEsa<TSpec> >&) [with TText = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = void]’ at ./external/seqan-library-2.2.0/include/seqan/index/index_shims.h:652:23,
- inlined from ‘seqan::Iter<TIndex, seqan::VSTree<seqan::TopDown<TSpec> > >::Iter(TIndex&) [with TIndex = seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > > >; TSpec = seqan::Preorder]’ at ./external/seqan-library-2.2.0/include/seqan/index/index_esa_stree.h:211:42,
- inlined from ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’ at src/adapter_removal.h:241:49:
-./external/seqan-library-2.2.0/include/seqan/basic/allocator_interface.h:230:33: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
- 230 | data = (TValue *) operator new(count * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/9/bits/exception_ptr.h:40,
- from /usr/include/c++/9/exception:143,
- from /usr/include/c++/9/ios:39,
- from /usr/include/c++/9/ostream:38,
- from /usr/include/c++/9/iostream:39,
- from src/popins2.cpp:1:
-/usr/include/c++/9/new: In function ‘typename seqan::Size<TRight>::Type prefixMatchLength(seqan::Index<TObject, TSpec>&, const TSequence&) [with TIndexSeq = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TSequence = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]’:
-/usr/include/c++/9/new:125:26: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
- 125 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Bam_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/stream.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Sam_]’:
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Sam_> >]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 159 | TLowcase lowcaseFileName(fileName);
- | ^~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/modifier.h:75,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:59,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
- 150 | ModifiedString(typename Parameter_<THost>::Type host):
- | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:95,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type seqan::_toPointer(seqan::Segment<THost, TSpec>&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_<seqan::Segment<THost, TSpec> >::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’:
-./external/seqan-library-2.2.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString<THost, seqan::ModView<TFunctor> >::ModifiedString(typename seqan::Parameter_<TContainer>::Type) [with THost = const seqan::Segment<const char*, seqan::PrefixSegment>; TFunctor = seqan::FunctorLowcase<const char, const char>; typename seqan::Parameter_<TContainer>::Type = seqan::Segment<const char*, seqan::PrefixSegment>]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag<TSpec>) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TFormat_ = seqan::Bam_]’
-./external/seqan-library-2.2.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector<TSubList>&) [with TFilename = seqan::Segment<const char*, seqan::PrefixSegment>; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:698:37: required from ‘bool seqan::_open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void; TThrowExceptions = seqan::False]’
-./external/seqan-library-2.2.0/include/seqan/stream/formatted_file.h:715:17: required from ‘bool seqan::open(seqan::FormattedFile<TFileFormat, TDirection, TSpec>&, const char*, int) [with TFileFormat = seqan::Tag<seqan::Bam_>; TDirection = seqan::Tag<seqan::Input_>; TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:648:35: required from here
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment<const char*, seqan::PrefixSegment>::Segment(const seqan::Segment<const char*, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy]
- 443 | return me;
- | ^~
-In file included from ./external/seqan-library-2.2.0/include/seqan/sequence.h:98,
- from ./external/seqan-library-2.2.0/include/seqan/file.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/stream.h:62,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:45,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment<const char*, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment<THost, seqan::PrefixSegment>& seqan::Segment<THost, seqan::PrefixSegment>::operator=(const seqan::Segment<THost, seqan::PrefixSegment>&) [with THost_ = const char*]’
- 117 | operator = (Segment const & source)
- | ^~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_fundamental.h:82,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:58,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:44,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayMoveForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’:
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1199:29: required from ‘void seqan::arrayMoveForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1047:21: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1066:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::reserve(seqan::String<TValue, TSpec>&, TSize_, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1725:45: required from ‘static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::Iupac_>, seqan::Alloc<> >; TExpand = seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/sequence/string_base.h:1785:50: required from ‘typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::Iupac_>; TSpec = seqan::Alloc<>; TSize = int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/read_bam.h:247:11: required from ‘void seqan::readRecord(seqan::BamAlignmentRecord&, seqan::BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>&, TForwardIter&, const Bam&) [with TForwardIter = seqan::Iter<seqan::VirtualStream<char, seqan::Tag<seqan::Input_> >, seqan::StreamIterator<seqan::Tag<seqan::Input_> > >; TNameStore = seqan::StringSet<seqan::String<char, seqan::Alloc<> > >; TNameStoreCache = seqan::NameStoreCache<seqan::StringSet<seqan::String<char, seqan::Alloc<> > > >; TStorageSpec = seqan::Dependent<seqan::Tag<seqan::TagInsist_> >; seqan::Bam = seqan::Tag<seqan::Bam_>]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_file.h:231:19: required from ‘void seqan::readRecord(seqan::BamAlignmentRecord&, seqan::BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>&, TForwardIter&, const seqan::TagSelector<TTagList>&) [with TForwardIter = seqan::Iter<seqan::VirtualStream<char, seqan::Tag<seqan::Input_> >, seqan::StreamIterator<seqan::Tag<seqan::Input_> > >; TNameStore = seqan::StringSet<seqan::String<char, seqan::Alloc<> > >; TNameStoreCache = seqan::NameStoreCache<seqan::StringSet<seqan::String<char, seqan::Alloc<> > > >; TStorageSpec = seqan::Dependent<seqan::Tag<seqan::TagInsist_> >; TTagList = seqan::TagList<seqan::Tag<seqan::Bam_>, seqan::TagList<seqan::Tag<seqan::Sam_> > >]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_file.h:241:15: required from ‘void seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Input_>, TSpec>&) [with TSpec = void]’
-./external/seqan-library-2.2.0/include/seqan/bam_io/bam_index_bai.h:670:35: required from here
-./external/seqan-library-2.2.0/include/seqan/basic/array_construct_destruct.h:1180:17: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
- 1180 | std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
- | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from ./external/seqan-library-2.2.0/include/seqan/basic/basic_alphabet.h:84,
- from ./external/seqan-library-2.2.0/include/seqan/basic/basic_container.h:47,
- from ./external/seqan-library-2.2.0/include/seqan/basic.h:71,
- from ./external/seqan-library-2.2.0/include/seqan/seq_io.h:44,
- from src/ColoredDeBruijnGraph.h:8,
- from src/LECC_Finder.h:13,
- from src/LECC_Finder.cpp:1:
-./external/seqan-library-2.2.0/include/seqan/basic/alphabet_simple_type.h:131:7: note: ‘class seqan::SimpleType<unsigned char, seqan::Iupac_>’ declared here
- 131 | class SimpleType
- | ^~~~~~~~~~
diff --git a/popins2.config b/popins2.config
deleted file mode 100644
index f9b89a8ddc38992f9a3db7d1b5e0324e2aba3380..0000000000000000000000000000000000000000
--- a/popins2.config
+++ /dev/null
@@ -1,15 +0,0 @@
-
-##########################################################
-# EDIT THIS FILE TO CONFIGURE POPINS2 BEFORE COMPILATION #
-##########################################################
-
-# Paths to binaries of external tools
-SAMTOOLS := samtools
-BWA := bwa
-SICKLE := sickle
-VELVETH := velveth-63
-VELVETG := velvetg-63
-MINIA := external/gatb-minia-pipeline/gatb
-
-##########################################################
-
diff --git a/src/argument_parsing.h b/src/argument_parsing.h
index 7add025f09e841300d95b81133d5572b9d57926d..bbd2c61764ba3dd0c2ddfbdeb0a404e0ba0d4149 100644
--- a/src/argument_parsing.h
+++ b/src/argument_parsing.h
@@ -20,40 +20,6 @@ using namespace std;
// Option wrapper classes
// =========================
-struct AssemblyOptions {
- CharString mappingFile;
- CharString matepairFile;
- CharString referenceFile;
-
- CharString prefix;
- CharString sampleID;
-
- unsigned kmerLength;
- CharString adapters;
- int humanSeqs;
-
- unsigned threads;
- CharString memory;
-
- bool use_velvet;
- bool skip_assembly;
- float alignment_score_factor;
-
- AssemblyOptions () :
- matepairFile(""),
- referenceFile(""),
- prefix("."),
- sampleID(""),
- kmerLength(47),
- humanSeqs(maxValue<int>()),
- threads(1),
- memory("768M"),
- use_velvet(false),
- skip_assembly(false),
- alignment_score_factor(0.67f)
- {}
-};
-
struct CropUnmappedOptions {
@@ -98,29 +64,6 @@ struct CropUnmappedOptions {
{}
};
-
-struct RemappingOptions {
- CharString sampleID;
- CharString referenceFile;
- CharString workingDir;
- unsigned humanSeqs;
- unsigned threads;
- CharString memory;
- CharString prefix;
- float alignment_score_factor;
-
- RemappingOptions():
- sampleID(""),
- referenceFile(""),
- workingDir(""),
- humanSeqs(maxValue<int>()),
- threads(1),
- memory("768M"),
- prefix("."),
- alignment_score_factor(0.67f)
- {}
-};
-
struct MergeSetMateOptions {
CharString prefix;
CharString sampleID;
@@ -196,49 +139,6 @@ struct MergeOptions {
};
-struct MultikOptions {
- int k_init;
- unsigned k_max;
- unsigned delta_k;
-
- vector<string> inputFiles;
-
- std::string samplePath;
- std::string tempPath;
-
- std::string prefixFilenameOut;
-
- MultikOptions () :
- k_init(27),
- k_max(127),
- delta_k(20),
- samplePath(""),
- tempPath("auxMultik"),
- prefixFilenameOut("ccdbg")
- {}
-};
-
-
-struct ContigMapOptions {
- CharString prefix;
- CharString sampleID;
- CharString contigFile;
- CharString referenceFile;
-
- bool bestAlignment;
- int maxInsertSize;
- bool deleteNonRefNew;
-
- unsigned threads;
- CharString memory;
-
- ContigMapOptions() :
- prefix("."), sampleID(""), contigFile("supercontigs.fa"), referenceFile("genome.fa"),
- bestAlignment(false), maxInsertSize(800), deleteNonRefNew(false), threads(1), memory("768M")
- {}
-};
-
-
struct FindLocationsOptions {
CharString prefix;
CharString sampleID;
@@ -336,38 +236,6 @@ struct GenotypingOptions {
// Option transfer functions
// =========================
-bool getOptionValues(AssemblyOptions & options, ArgumentParser const & parser){
-
- getArgumentValue(options.mappingFile, parser, 0);
-
- if (isSet(parser, "prefix"))
- getOptionValue(options.prefix, parser, "prefix");
- if (isSet(parser, "sample"))
- getOptionValue(options.sampleID, parser, "sample");
- if (isSet(parser, "matePair"))
- getOptionValue(options.matepairFile, parser, "matePair");
- if (isSet(parser, "adapters"))
- getOptionValue(options.adapters, parser, "adapters");
- if (isSet(parser, "reference"))
- getOptionValue(options.referenceFile, parser, "reference");
- if (isSet(parser, "filter"))
- getOptionValue(options.humanSeqs, parser, "filter");
- if (isSet(parser, "use-velvet"))
- getOptionValue(options.use_velvet, parser, "use-velvet");
- if (isSet(parser, "skip-assembly"))
- getOptionValue(options.skip_assembly, parser, "skip-assembly");
- if (isSet(parser, "kmerLength"))
- getOptionValue(options.kmerLength, parser, "kmerLength");
- if (isSet(parser, "threads"))
- getOptionValue(options.threads, parser, "threads");
- if (isSet(parser, "memory"))
- getOptionValue(options.memory, parser, "memory");
- if (isSet(parser, "alignment-score-factor"))
- getOptionValue(options.alignment_score_factor, parser, "alignment-score-factor");
-
- return true;
-}
-
bool getOptionValues(CropUnmappedOptions & options, ArgumentParser const & parser){
getArgumentValue(options.mappingFile, parser, 0);
@@ -407,25 +275,6 @@ bool getOptionValues(CropUnmappedOptions & options, ArgumentParser const & parse
return true;
}
-bool getOptionValues(RemappingOptions & options, ArgumentParser const & parser){
-
-
- if (isSet(parser, "prefix"))
- getOptionValue(options.prefix, parser, "prefix");
- if (isSet(parser, "sample"))
- getOptionValue(options.sampleID, parser, "sample");
- if (isSet(parser, "reference"))
- getOptionValue(options.referenceFile, parser, "reference");
- if (isSet(parser, "threads"))
- getOptionValue(options.threads, parser, "threads");
- if (isSet(parser, "memory"))
- getOptionValue(options.memory, parser, "memory");
- if (isSet(parser, "alignment-score-factor"))
- getOptionValue(options.alignment_score_factor, parser, "alignment-score-factor");
-
- return true;
-}
-
bool getOptionValues(MergeSetMateOptions & options, ArgumentParser const & parser){
getArgumentValue(options.nonRefBam, parser, 0);
@@ -517,52 +366,6 @@ void setupBifrostOptions(const MergeOptions &options, CCDBG_Build_opt &graph_opt
}
-bool getOptionValues(MultikOptions &options, seqan::ArgumentParser &parser){
- if (isSet(parser, "sample-path")){
- // store sample path
- getOptionValue(options.samplePath, parser, "sample-path");
- // get fastx files from sample path
- getFastx(options.inputFiles, options.samplePath);
- }
- if (isSet(parser, "temp-path"))
- getOptionValue(options.tempPath, parser, "temp-path");
- if (isSet(parser, "outputfile-prefix"))
- getOptionValue(options.prefixFilenameOut, parser, "outputfile-prefix");
- if (isSet(parser, "k-init"))
- getOptionValue(options.k_init, parser, "k-init");
- if (isSet(parser, "k-max"))
- getOptionValue(options.k_max, parser, "k-max");
- if (isSet(parser, "delta-k"))
- getOptionValue(options.delta_k, parser, "delta-k");
-
- return true;
-}
-
-
-bool getOptionValues(ContigMapOptions &options, seqan::ArgumentParser &parser){
- getArgumentValue(options.sampleID, parser, 0);
-
- if (isSet(parser, "prefix"))
- getOptionValue(options.prefix, parser, "prefix");
- if (isSet(parser, "contigs"))
- getOptionValue(options.contigFile, parser, "contigs");
- if (isSet(parser, "reference"))
- getOptionValue(options.referenceFile, parser, "reference");
- if (isSet(parser, "best"))
- options.bestAlignment = true;
- if (isSet(parser, "maxInsertSize"))
- getOptionValue(options.maxInsertSize, parser, "maxInsertSize");
- if (isSet(parser, "noNonRefNew"))
- options.deleteNonRefNew = true;
- if (isSet(parser, "threads"))
- getOptionValue(options.threads, parser, "threads");
- if (isSet(parser, "memory"))
- getOptionValue(options.memory, parser, "memory");
-
- return true;
-}
-
-
bool getOptionValues(FindLocationsOptions &options, seqan::ArgumentParser &parser){
getArgumentValue(options.sampleID, parser, 0);
@@ -694,22 +497,12 @@ bool getOptionValues(GenotypingOptions &options, seqan::ArgumentParser &parser){
// Hide options functions
// =========================
-void setHiddenOptions(ArgumentParser & parser, bool hide, AssemblyOptions &){
- hideOption(parser, "matePair", hide);
- hideOption(parser, "kmerLength", hide);
- hideOption(parser, "alignment-score-factor", hide);
-}
-
void setHiddenOptions(ArgumentParser & parser, bool hide, CropUnmappedOptions &){
hideOption(parser, "matePair", hide);
hideOption(parser, "kmerLength", hide);
hideOption(parser, "alignment-score-factor", hide);
}
-void setHiddenOptions(ArgumentParser & parser, bool hide, RemappingOptions &){
- hideOption(parser, "alignment-score-factor", hide);
-}
-
void setHiddenOptions(seqan::ArgumentParser & /*parser*/, bool /*hide*/, MergeSetMateOptions &){
// TODO
}
@@ -724,19 +517,6 @@ void setHiddenOptions(seqan::ArgumentParser &parser, bool hide, MergeOptions &){
hideOption(parser, "write-lecc", hide);
}
-
-void setHiddenOptions(seqan::ArgumentParser & /*parser*/, bool /*hide*/, MultikOptions &){
- // TODO
-}
-
-
-void setHiddenOptions(seqan::ArgumentParser &parser, bool hide, ContigMapOptions &){
- hideOption(parser, "b", hide);
- hideOption(parser, "e", hide);
- hideOption(parser, "d", hide);
-}
-
-
void setHiddenOptions(seqan::ArgumentParser & /*parser*/, bool /*hide*/, FindLocationsOptions &){
// TODO
}
@@ -776,59 +556,6 @@ void setHiddenOptions(seqan::ArgumentParser &parser, bool hide, GenotypingOption
// Functions setupParser()
// ==========================================================================
-void setupParser(ArgumentParser & parser, AssemblyOptions & options){
- setShortDescription(parser, "Assembly of unmapped reads.");
- setVersion(parser, VERSION);
- setDate(parser, DATE);
-
- // Define usage line and long description.
- addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fIBAM_FILE\\fP");
- addDescription(parser, "Finds reads without high-quality alignment in the \\fIBAM FILE\\fP, quality filters them "
- "using SICKLE and assembles them into contigs using MINIA (default) or VELVET. If the option "
- "\'--reference \\fIFASTA FILE\\fP\' is set, the reads are first remapped to this reference using BWA-MEM and "
- "only reads that remain without high-quality alignment after remapping are quality-filtered and assembled.");
-
- // Require a bam file as argument.
- addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "BAM_FILE"));
-
- // Setup the options.
- addSection(parser, "Input/output options");
- addOption(parser, ArgParseOption("p", "prefix", "Path to the sample directories.", ArgParseArgument::STRING, "PATH"));
- addOption(parser, ArgParseOption("s", "sample", "An ID for the sample.", ArgParseArgument::STRING, "SAMPLE_ID"));
- addOption(parser, ArgParseOption("mp", "matePair", "(Currently only available for Velvet.)", ArgParseArgument::INPUT_FILE, "BAM FILE"));
-
- addSection(parser, "Algorithm options");
- addOption(parser, ArgParseOption("a", "adapters", "Enable adapter removal for Illumina reads. Default: \\fIno adapter removal\\fP.", ArgParseArgument::STRING, "STR"));
- addOption(parser, ArgParseOption("r", "reference", "Remap reads to this reference before assembly. Default: \\fIno remapping\\fP.", ArgParseArgument::INPUT_FILE, "FASTA_FILE"));
- addOption(parser, ArgParseOption("f", "filter", "Treat reads aligned to all but the first INT reference sequences after remapping as high-quality aligned even if their alignment quality is low. "
- "Recommended for non-human reference sequences.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("vel", "use-velvet", "Use the velvet assembler. Default: Minia."));
- addOption(parser, ArgParseOption("n", "skip-assembly", "Skip assembly per sample."));
- addOption(parser, ArgParseOption("k", "kmerLength", "The k-mer size if the velvet assembler is used.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("c", "alignment-score-factor", "A record is considered low quality if the alignment score (AS) is below FLOAT*read length", seqan::ArgParseArgument::DOUBLE, "FLOAT"));
- addSection(parser, "Compute resource options");
- addOption(parser, ArgParseOption("t", "threads", "Number of threads to use for BWA and samtools sort.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("m", "memory", "Maximum memory per thread for samtools sort; suffix K/M/G recognized.", ArgParseArgument::STRING, "STR"));
-
- // Set valid and default values.
- setValidValues(parser, "adapters", "HiSeq HiSeqX");
- setValidValues(parser, "reference", "fa fna fasta gz");
- setDefaultValue(parser, "prefix", "\'.\'");
- setDefaultValue(parser, "sample", "retrieval from BAM file header");
- setDefaultValue(parser, "kmerLength", options.kmerLength);
- setDefaultValue(parser, "threads", options.threads);
- setDefaultValue(parser, "memory", options.memory);
- setDefaultValue(parser, "alignment-score-factor", options.alignment_score_factor);
-
- setMinValue(parser, "threads", "1");
- setMinValue(parser, "alignment-score-factor", "0.0");
- setMaxValue(parser, "alignment-score-factor", "1.0");
-
- // Hide some options from default help.
- setHiddenOptions(parser, true, options);
-}
-
-
void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
setShortDescription(parser, "Crop unmapped reads.");
@@ -891,55 +618,6 @@ void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
}
-void setupParser(ArgumentParser & parser, RemappingOptions & options){
- setShortDescription(parser, "Assembly of unmapped reads.");
- setVersion(parser, VERSION);
- setDate(parser, DATE);
-
- // Define usage line and long description.
- addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fIBAM_FILE\\fP");
- addDescription(parser, "Finds reads without high-quality alignment in the \\fIBAM FILE\\fP, quality filters them "
- "using SICKLE and assembles them into contigs using MINIA (default) or VELVET. If the option "
- "\'--reference \\fIFASTA FILE\\fP\' is set, the reads are first remapped to this reference using BWA-MEM and "
- "only reads that remain without high-quality alignment after remapping are quality-filtered and assembled.");
-
- // Require a bam file as argument.
- addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "BAM_FILE"));
-
- // Setup the options.
- addSection(parser, "Input/output options");
- addOption(parser, ArgParseOption("p", "prefix", "Path to the sample directories.", ArgParseArgument::STRING, "PATH"));
- addOption(parser, ArgParseOption("s", "sample", "An ID for the sample.", ArgParseArgument::STRING, "SAMPLE_ID"));
- addOption(parser, ArgParseOption("mp", "matePair", "(Currently only available for Velvet.)", ArgParseArgument::INPUT_FILE, "BAM FILE"));
-
- addSection(parser, "Algorithm options");
- addOption(parser, ArgParseOption("a", "adapters", "Enable adapter removal for Illumina reads. Default: \\fIno adapter removal\\fP.", ArgParseArgument::STRING, "STR"));
- addOption(parser, ArgParseOption("r", "reference", "Remap reads to this reference before assembly. Default: \\fIno remapping\\fP.", ArgParseArgument::INPUT_FILE, "FASTA_FILE"));
- addOption(parser, ArgParseOption("f", "filter", "Treat reads aligned to all but the first INT reference sequences after remapping as high-quality aligned even if their alignment quality is low. "
- "Recommended for non-human reference sequences.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("c", "alignment-score-factor", "A record is considered low quality if the alignment score (AS) is below FLOAT*read length", seqan::ArgParseArgument::DOUBLE, "FLOAT"));
- addSection(parser, "Compute resource options");
- addOption(parser, ArgParseOption("t", "threads", "Number of threads to use for BWA and samtools sort.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("m", "memory", "Maximum memory per thread for samtools sort; suffix K/M/G recognized.", ArgParseArgument::STRING, "STR"));
-
- // Set valid and default values.
- setValidValues(parser, "adapters", "HiSeq HiSeqX");
- setValidValues(parser, "reference", "fa fna fasta gz");
- setDefaultValue(parser, "prefix", "\'.\'");
- setDefaultValue(parser, "sample", "retrieval from BAM file header");
- setDefaultValue(parser, "threads", options.threads);
- setDefaultValue(parser, "memory", options.memory);
- setDefaultValue(parser, "alignment-score-factor", options.alignment_score_factor);
-
- setMinValue(parser, "threads", "1");
- setMinValue(parser, "alignment-score-factor", "0.0");
- setMaxValue(parser, "alignment-score-factor", "1.0");
-
- // Hide some options from default help.
- setHiddenOptions(parser, true, options);
-}
-
-
void setupParser(ArgumentParser & parser, MergeSetMateOptions & options){
setShortDescription(parser, "Find the other reads in pairs for remapped reads."); // TODO: are the "other reads" the "mates"?
setVersion(parser, VERSION);
@@ -1034,84 +712,6 @@ void setupParser(seqan::ArgumentParser &parser, MergeOptions &options){
}
-void setupParser(seqan::ArgumentParser &parser, MultikOptions &options){
- // Setup meta-information
- seqan::setShortDescription(parser, "Multi-k framework for a colored and compacted de Bruijn Graph (CCDBG)");
- seqan::setVersion(parser, VERSION);
- seqan::setDate(parser, DATE);
- seqan::addUsageLine(parser, "\\--sample-path STRING [OPTIONS] \\fP ");
-
- // Setup options
- seqan::addSection(parser, "I/O options");
- seqan::addOption(parser, seqan::ArgParseOption("s", "sample-path", "Source directory with FASTA/Q files", seqan::ArgParseArgument::STRING, "DIR"));
- seqan::addOption(parser, seqan::ArgParseOption("a", "temp-path", "Auxiliary directory for temporary files.", seqan::ArgParseArgument::STRING, "DIR"));
- seqan::addOption(parser, seqan::ArgParseOption("p", "outputfile-prefix", "Specify a prefix for the output files", seqan::ArgParseArgument::STRING, "STRING"));
-
- seqan::addSection(parser, "Algorithm options");
- seqan::addOption(parser, seqan::ArgParseOption("k", "k-init", "Initial kmer length to start the multi-k iteration", seqan::ArgParseArgument::INTEGER, "INT"));
- seqan::addOption(parser, seqan::ArgParseOption("m", "k-max", "Maximal kmer length to build a dBG with", seqan::ArgParseArgument::INTEGER, "INT"));
- seqan::addOption(parser, seqan::ArgParseOption("d", "delta-k", "Step size to increase k", seqan::ArgParseArgument::INTEGER, "INT"));
-
- // Setup option constraints
- seqan::setDefaultValue(parser, "p", options.prefixFilenameOut);
- seqan::setDefaultValue(parser, "a", options.tempPath);
- seqan::setDefaultValue(parser, "k", options.k_init);
- seqan::setDefaultValue(parser, "m", options.k_max);
- seqan::setDefaultValue(parser, "d", options.delta_k);
-
- // Setup hidden options
- setHiddenOptions(parser, true, options);
-}
-
-
-void setupParser(seqan::ArgumentParser &parser, ContigMapOptions &options){
- setShortDescription(parser, "Alignment of unmapped reads to assembled contigs.");
- setVersion(parser, VERSION);
- setDate(parser, DATE);
-
- // Define usage line and long description.
- addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fISAMPLE_ID\\fP");
- addDescription(parser, "Aligns the reads with low-quality alignments of a sample to the set of supercontigs using "
- "BWA-MEM. Merges the BWA output file with the sample's non_ref.bam file into a non_ref_new.bam file where "
- "information about read mates is set.");
-
- addArgument(parser, ArgParseArgument(ArgParseArgument::STRING, "SAMPLE_ID"));
-
- // Setup the options.
- addSection(parser, "Input/output options");
- addOption(parser, ArgParseOption("p", "prefix", "Path to the sample directories.", ArgParseArgument::STRING, "PATH"));
- addOption(parser, ArgParseOption("c", "contigs", "Name of (super-)contigs file.", ArgParseArgument::INPUT_FILE, "FASTA_FILE"));
- addOption(parser, ArgParseOption("r", "reference", "Name of reference genome file.", ArgParseArgument::INPUT_FILE, "FASTA_FILE"));
-
- addSection(parser, "Algorithm options");
- addOption(parser, ArgParseOption("b", "best", "Do not use BWA-mem's -a option to output all alignments of a read."));
- addOption(parser, ArgParseOption("e", "maxInsertSize", "The maximum expected insert size of the read pairs.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("d", "noNonRefNew", "Delete the non_ref_new.bam file after writing locations."));
-
- addSection(parser, "Compute resource options");
- addOption(parser, ArgParseOption("t", "threads", "Number of threads to use for BWA and samtools sort.", ArgParseArgument::INTEGER, "INT"));
- addOption(parser, ArgParseOption("m", "memory", "Maximum memory per thread for samtools sort; suffix K/M/G recognized.", ArgParseArgument::STRING, "STR"));
-
- // Set valid values.
- setMinValue(parser, "threads", "1");
- setValidValues(parser, "reference", "fa fna fasta");
- setValidValues(parser, "contigs", "fa fna fasta");
-
- // Set default values.
- setDefaultValue(parser, "prefix", "\'.\'");
- setDefaultValue(parser, "contigs", options.contigFile);
- setDefaultValue(parser, "reference", options.referenceFile);
- setDefaultValue(parser, "best", "false");
- setDefaultValue(parser, "maxInsertSize", options.maxInsertSize);
- setDefaultValue(parser, "noNonRefNew", "false");
- setDefaultValue(parser, "threads", options.threads);
- setDefaultValue(parser, "memory", options.memory);
-
- // Hide some options from default help.
- setHiddenOptions(parser, true, options);
-}
-
-
void setupParser(seqan::ArgumentParser &parser, FindLocationsOptions &options){
setShortDescription(parser, "Find insertion locations per sample.");
setVersion(parser, VERSION);
@@ -1359,39 +959,6 @@ void setupParser(seqan::ArgumentParser &parser, GenotypingOptions &options){
// Function checkInput()
// ==========================================================================
-ArgumentParser::ParseResult checkInput(AssemblyOptions & options){
-
- ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
-
- if (options.prefix != "." && !exists(options.prefix))
- {
- std::cerr << "ERROR: Path to sample directories \'" << options.prefix << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (!exists(options.mappingFile))
- {
- std::cerr << "ERROR: Input BAM file \'" << options.mappingFile << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- CharString baiFile = options.mappingFile;
- baiFile += ".bai";
- if (!exists(baiFile))
- {
- std::cerr << "ERROR: BAM index file \'" << baiFile << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (options.matepairFile != "" && !exists(options.matepairFile))
- {
- std::cerr << "ERROR: Input BAM file \'" << options.matepairFile << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- return res;
-}
-
ArgumentParser::ParseResult checkInput(CropUnmappedOptions & options){
ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
@@ -1426,21 +993,6 @@ ArgumentParser::ParseResult checkInput(CropUnmappedOptions & options){
}
-ArgumentParser::ParseResult checkInput(RemappingOptions & options){
-
- ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
-
- if (options.prefix != "." && !exists(options.prefix))
- {
- std::cerr << "ERROR: Path to sample directories \'" << options.prefix << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
-
- return res;
-}
-
-
ArgumentParser::ParseResult checkInput(MergeSetMateOptions & options){
ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
@@ -1495,8 +1047,8 @@ ArgumentParser::ParseResult checkInput(MergeOptions & options){
res = ArgumentParser::PARSE_ERROR;
}
- if (strcmp(options.filename_graph_in.c_str(), "")!=0 && strcmp(options.filename_colors_in.c_str(), "")==0 ||
- strcmp(options.filename_graph_in.c_str(), "")==0 && strcmp(options.filename_colors_in.c_str(), "")!=0){
+ if ((strcmp(options.filename_graph_in.c_str(), "")!=0 && strcmp(options.filename_colors_in.c_str(), "")==0) ||
+ (strcmp(options.filename_graph_in.c_str(), "")==0 && strcmp(options.filename_colors_in.c_str(), "")!=0)){
cerr << "[popins2 merge][parser] ERROR: One of the colored de Bruijn Graph files is missing (-y/-z)." << endl;
cerr << "[popins2 merge][parser] ERROR: If a graph should be read, please provide a graph (-y) AND a colors file (-z)." << endl;
res = ArgumentParser::PARSE_ERROR;
@@ -1511,65 +1063,6 @@ ArgumentParser::ParseResult checkInput(MergeOptions & options){
}
-ArgumentParser::ParseResult checkInput(MultikOptions & options){
-
- ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
-
- if (options.samplePath == "") {
- cerr << "[popins2 multik][parser] ERROR: No input path specified." << endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (options.k_init < 1) {
- cerr << "[popins2 multik][parser] ERROR: Parameter k_init must be a positive integer." << endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if ((unsigned)options.k_init > options.k_max) {
- cerr << "[popins2 multik][parser] ERROR: Parameter k_init must be smaller than k_max." << endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (options.delta_k > options.k_max) {
- cerr << "[popins2 multik][parser] ERROR: Parameter delta_k must be smaller than k_max." << endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (options.delta_k > (options.k_max - (unsigned)options.k_init)) {
- cerr << "[popins2 multik][parser] ERROR: This step size delta_k will have no effect." << endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- return res;
-}
-
-
-ArgumentParser::ParseResult checkInput(ContigMapOptions &options){
-
- ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
-
- if (options.prefix != "." && !exists(options.prefix))
- {
- std::cerr << "ERROR: Path to sample directories \'" << options.prefix << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (!exists(options.contigFile))
- {
- std::cerr << "ERROR: Contig file \'" << options.contigFile << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- if (!exists(options.referenceFile))
- {
- std::cerr << "ERROR: Reference genome file \'" << options.referenceFile << "\' does not exist." << std::endl;
- res = ArgumentParser::PARSE_ERROR;
- }
-
- return res;
-}
-
-
ArgumentParser::ParseResult checkInput(FindLocationsOptions &options){
ArgumentParser::ParseResult res = ArgumentParser::PARSE_OK;
@@ -1711,10 +1204,7 @@ void printHelp(char const * name){
std::cerr << "\033[1mCOMMAND\033[0m" << std::endl;
std::cerr << " \033[1mcrop-unmapped\033[0m Clip unmapped and poorly aligned reads from a sample." << std::endl;
std::cerr << " \033[1mmerge-set-mate\033[0m Merge and mate poorly aligned reads into contigs." << std::endl;
- std::cerr << " \033[1mremapping\033[0m Remap sample to reference (optional)." << std::endl;
std::cerr << " \033[1mmerge\033[0m Generate supercontigs from a colored compacted de Bruijn Graph." << std::endl;
- std::cerr << " \033[1mmultik\033[0m Multi-k framework for a colored compacted de Bruijn Graph." << std::endl;
- std::cerr << " \033[1mcontigmap\033[0m Map unmapped reads to (super-)contigs." << std::endl;
std::cerr << " \033[1mfind-locations\033[0m Find insertion locations per individual." << std::endl;
std::cerr << " \033[1mplace-refalign\033[0m Find position of (super-)contigs by aligning contig ends to the reference genome." << std::endl;
std::cerr << " \033[1mplace-splitalign\033[0m Find position of (super-)contigs by split-read alignment (per sample)." << std::endl;
@@ -1752,22 +1242,6 @@ void printMergeOptions(const MergeOptions &options){
cout << "=========================================================" << endl;
}
-
-void printMultikOptions(const MultikOptions &options){
- cout << "=========================================================" << endl;
- cout << "popins2 version : " << VERSION << endl;
- cout << "PARAMETER ======== : VALUE ==============================" << endl;
- cout << "sample-path : " << options.samplePath << endl;
- cout << "#input files : " << options.inputFiles.size() << endl;
- cout << "temp-path : " << options.tempPath << endl;
- cout << "outputfile-prefix : " << options.prefixFilenameOut << endl;
- cout << "k-init : " << options.k_init << endl;
- cout << "k-max : " << options.k_max << endl;
- cout << "delta-k : " << options.delta_k << endl;
- cout << "=========================================================" << endl;
-}
-
-
void printFindLocationsOptions(const FindLocationsOptions &options){
cout << "==========================================================" << endl;
cout << "popins version : " << VERSION << endl;
diff --git a/src/out.txt b/src/out.txt
deleted file mode 100644
index 33edf65aab6e7a4778f160dde6585216181c4cfb..0000000000000000000000000000000000000000
--- a/src/out.txt
+++ /dev/null
@@ -1 +0,0 @@
-make: *** No targets specified and no makefile found. Stop.
diff --git a/src/popins2.h b/src/popins2.h
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/src/popins2_assemble.h b/src/popins2_assemble.h
deleted file mode 100644
index 96e30d783e826a4109ce523715571f74c9028a02..0000000000000000000000000000000000000000
--- a/src/popins2_assemble.h
+++ /dev/null
@@ -1,687 +0,0 @@
-#include <sstream>
-#include <cerrno>
-
-#include <seqan/file.h>
-#include <seqan/sequence.h>
-
-#include "util.h"
-#include "argument_parsing.h"
-#include "crop_unmapped.h"
-
-#ifndef POPINS_ASSEMBLE_H_
-#define POPINS_ASSEMBLE_H_
-
-using namespace seqan;
-
-// ==========================================================================
-
-inline void
-removeAssemblyDirectory(CharString & path)
-{
- removeFile(path, "contigs.fa");
- removeFile(path, "Graph2");
- removeFile(path, "LastGraph");
- removeFile(path, "Log");
- removeFile(path, "PreGraph");
- removeFile(path, "Roadmaps");
- removeFile(path, "Sequences");
- removeFile(path, "stats.txt");
- remove(toCString(path));
-}
-
-bool retrieveSampleID(CharString & sampleID, CharString & mappingBam)
-{
- BamFileIn inStream(toCString(mappingBam));
-
- BamHeader header;
- readHeader(header, inStream);
-
- for (unsigned i = 0; i < length(header); ++i)
- {
- if (header[i].type != BamHeaderRecordType::BAM_HEADER_READ_GROUP)
- continue;
-
- for (unsigned j = 0; j < length(header[i].tags); ++j)
- {
- if (header[i].tags[j].i1 != "SM")
- continue;
-
- sampleID = header[i].tags[j].i2;
- return 0;
- }
- }
- std::cerr << "ERROR: Could not find sample ID in BAM file header." << std::endl;
- return 1;
-}
-
-// ==========================================================================
-// Function remapping()
-// ==========================================================================
-
-inline int remapping(Triple<CharString> & fastqFilesTemp,
- Triple<CharString> & fastqFiles,
- CharString const & referenceFile,
- CharString const & workingDir,
- unsigned humanSeqs,
- unsigned threads,
- CharString & memory,
- CharString & prefix,
- float as_factor)
-{
- std::stringstream cmd;
-
- CharString f1 = prefix;
- f1 += "remapped.sam";
- CharString remappedSam = getFileName(workingDir, f1);
-
- CharString f2 = prefix;
- f2 += "remapped.bam";
- CharString remappedBam = getFileName(workingDir, f2);
-
- CharString f3 = prefix;
- f3 += "remapped.bam.bai";
- CharString remappedBai = getFileName(workingDir, f3);
-
- CharString f4 = prefix;
- f4 += "remapped_unsorted.bam";
- CharString remappedUnsortedBam = getFileName(workingDir, f4);
-
- std::ostringstream msg;
- msg << "Remapping unmapped reads using " << BWA;
- printStatus(msg);
-
- // Run BWA on unmapped reads (pairs).
- cmd.str("");
- cmd << BWA << " mem -t " << threads << " " << referenceFile << " " << fastqFilesTemp.i1 << " " << fastqFilesTemp.i2 << " > " << remappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFilesTemp.i1 << " and " << fastqFilesTemp.i2 << std::endl;
- return 1;
- }
-
- remove(toCString(fastqFilesTemp.i1));
- remove(toCString(fastqFilesTemp.i2));
-
- // Run BWA on unmapped reads (single end).
- cmd.str("");
- cmd << BWA << " mem -t " << threads << " " << referenceFile << " " << fastqFilesTemp.i3 << " | awk '$1 !~ /@/' >> " << remappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFilesTemp.i3 << std::endl;
- return 1;
- }
-
- remove(toCString(fastqFilesTemp.i3));
-
- msg.str("");
- msg << "Converting BWA output " << remappedSam << " to bam format.";
- printStatus(msg);
-
- // Convert BWA output to bam.
- cmd.str("");
- cmd << SAMTOOLS << " view -S -h -b " << remappedSam << " > " << remappedUnsortedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while converting BWA output " << remappedSam << " to bam." << std::endl;
- return 1;
- }
- remove(toCString(remappedSam));
-
- msg.str("");
- msg << "Sorting " << remappedUnsortedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort bam file.
- cmd.str("");
- cmd << SAMTOOLS << " sort -@ " << threads << " -m " << memory << " -o " << remappedBam << " " << remappedUnsortedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting BWA output " << remappedUnsortedBam << std::endl;
- return 1;
- }
-
- msg.str("");
- msg << "Indexing " << remappedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Index bam file.
- cmd.str("");
- cmd << SAMTOOLS << " index " << remappedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while indexing BWA output " << remappedBam << std::endl;
- return 1;
- }
-
- msg.str("");
- msg << "Cropping unmapped reads from " << remappedBam;
- printStatus(msg);
-
- // Crop unmapped and create bam file of remapping.
- if (crop_unmapped(fastqFiles, remappedUnsortedBam, remappedBam, humanSeqs, NoAdapters(), as_factor) != 0)
- return 1;
- remove(toCString(remappedBai));
-
- msg.str("");
- msg << "Sorting " << remappedUnsortedBam << " by read name using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/remapped.bam by read name.
- cmd.str("");
- cmd << SAMTOOLS << " sort -n -@ " << threads << " -m " << memory << " -o " << remappedBam << " " << remappedUnsortedBam << " ";
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << remappedUnsortedBam << std::endl;
- return 1;
- }
-
- remove(toCString(remappedUnsortedBam));
-
- return 0;
-}
-
-// ==========================================================================
-
-inline void setMates(BamAlignmentRecord & record1, BamAlignmentRecord & record2) {
- SEQAN_ASSERT(!hasFlagFirst(record1) || !hasFlagFirst(record2));
- SEQAN_ASSERT(!hasFlagLast(record1) || !hasFlagLast(record2));
-
- // Set the next ref id.
- record1.rNextId = record2.rID;
- record2.rNextId = record1.rID;
-
- // Set the next ref pos.
- record1.pNext = record2.beginPos;
- record2.pNext = record1.beginPos;
-
- // Fix the next unmapped flag.
- if (hasFlagUnmapped(record2)) record1.flag |= BAM_FLAG_NEXT_UNMAPPED;
- else record1.flag &= ~BAM_FLAG_NEXT_UNMAPPED;
- if (hasFlagUnmapped(record1)) record2.flag |= BAM_FLAG_NEXT_UNMAPPED;
- else record2.flag &= ~BAM_FLAG_NEXT_UNMAPPED;
-
- // Fix the next reversed flag.
- if (hasFlagRC(record2)) record1.flag |= BAM_FLAG_NEXT_RC;
- else record1.flag &= ~BAM_FLAG_NEXT_RC;
- if (hasFlagRC(record1)) record2.flag |= BAM_FLAG_NEXT_RC;
- else record2.flag &= ~BAM_FLAG_NEXT_RC;
-
- // Fix first/second in pair flags.
- if (hasFlagFirst(record1)) record2.flag |= BAM_FLAG_LAST;
- if (hasFlagFirst(record2)) record1.flag |= BAM_FLAG_LAST;
- if (hasFlagLast(record1)) record2.flag |= BAM_FLAG_FIRST;
- if (hasFlagLast(record2)) record1.flag |= BAM_FLAG_FIRST;
-
- // Set flag paired.
- record1.flag |= BAM_FLAG_MULTIPLE;
- record2.flag |= BAM_FLAG_MULTIPLE;
-}
-
-// ==========================================================================
-
-// Correct the reference ids of a BamAlignmentRecord for the concatenated header.
-template<typename TNameStore>
-inline void readRecordAndCorrectRIds(BamAlignmentRecord & record, BamFileIn & stream, NameStoreCache<TNameStore> & nameStoreCache){
- readRecord(record, stream);
-
- if (record.rID != BamAlignmentRecord::INVALID_REFID)
- {
- CharString rName = contigNames(context(stream))[record.rID];
- getIdByName(record.rID, nameStoreCache, rName);
- }
- if (record.rNextId != BamAlignmentRecord::INVALID_REFID)
- {
- CharString rNextName = contigNames(context(stream))[record.rNextId];
- getIdByName(record.rNextId, nameStoreCache, rNextName);
- }
-}
-
-// ==========================================================================
-
-inline void mergeHeaders(BamHeader & header, FormattedFileContext<BamFileOut, Owner<> >::Type & context, BamFileIn & stream1, BamFileIn & stream2){
- StringSet<CharString> contigNames;
- NameStoreCache<StringSet<CharString> > nameStoreCache;
- String<int32_t> contigLengths;
-
- // Read and append the two headers. Remove duplicate entries.
- readHeader(header, stream1);
- BamHeader header2;
- readHeader(header2, stream2);
- for (unsigned i = 0; i < length(header2); ++i)
- {
- if (header2[i].type != BAM_HEADER_FIRST)
- appendValue(header, header2[i]);
- }
- std::stable_sort(begin(header, Standard()), end(header, Standard()), BamHeaderRecordTypeLess());
-
- // Fill sequence names into nameStoreCache.
- for (unsigned i = 0; i < length(header); ++i)
- {
- if (header[i].type == BAM_HEADER_REFERENCE)
- {
- CharString name, len;
- for (unsigned j = 0; j < length(header[i].tags); ++j)
- {
- if (header[i].tags[j].i1 == "SN")
- name = header[i].tags[j].i2;
- else if (header[i].tags[j].i1 == "LN")
- len = header[i].tags[j].i2;
- }
- appendName(context._contigNamesCache, name);
- int32_t l;
- lexicalCast<int32_t>(l, len);
- appendValue(context._contigLengths, l);
- }
- }
-}
-
-// ==========================================================================
-
-// This function is adapted from samtools code (fuction strnum_cmp in bam_sort.c) to ensure the exact same sort order.
-int
-compare_qName(CharString & nameA, CharString & nameB)
-{
- const char * _a = toCString(nameA);
- const char * _b = toCString(nameB);
- const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
- const unsigned char *pa = a, *pb = b;
- while (*pa && *pb) {
- if (isdigit(*pa) && isdigit(*pb)) {
- while (*pa == '0') ++pa;
- while (*pb == '0') ++pb;
- while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
- if (isdigit(*pa) && isdigit(*pb)) {
- int i = 0;
- while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
- return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
- } else if (isdigit(*pa)) return 1;
- else if (isdigit(*pb)) return -1;
- else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
- } else {
- if (*pa != *pb) return (int)*pa - (int)*pb;
- ++pa; ++pb;
- }
- }
- return *pa? 1 : *pb? -1 : 0;
-}
-
-// ==========================================================================
-// Function merge_and_set_mate()
-// ==========================================================================
-
-bool
-merge_and_set_mate(CharString &mergedBam, unsigned &nonContigSeqs, CharString &nonRefBam, CharString &remappedBam)
-{
- std::ostringstream msg;
- msg << "Merging bam files " << nonRefBam << " and " << remappedBam;
- printStatus(msg);
-
- // Open the two input streams (can read SAM and BAM files).
- BamFileIn nonRefStream(toCString(nonRefBam));
- BamFileIn remappedStream(toCString(remappedBam));
-
- printStatus(" - merging headers...");
-
- // Prepare a header for the output file.
- BamHeader outHeader;
- FormattedFileContext<BamFileOut, Owner<> >::Type bamContext;
- mergeHeaders(outHeader, bamContext, nonRefStream, remappedStream);
-
- printStatus(" - writing header...");
-
- // Open the output stream and write the header.
- FormattedFileContext<BamFileOut, Dependent<> >::Type bamContextDep(bamContext);
- BamFileOut outStream(bamContextDep, toCString(mergedBam));
- writeHeader(outStream, outHeader);
-
- nonContigSeqs = length(contigNames(context(nonRefStream)));
-
- printStatus(" - merging read records...");
-
- // Read the first record from each input file. Correct ids in records from remappedStreams for new header.
- BamAlignmentRecord record1, record2;
- if (!atEnd(nonRefStream)) readRecordAndCorrectRIds(record1, nonRefStream, contigNamesCache(bamContextDep));
- else record1.qName = "*";
- if (!atEnd(remappedStream)) readRecordAndCorrectRIds(record2, remappedStream, contigNamesCache(bamContextDep));
- else record2.qName = "*";
-
- // Iterate both input files, set mate positions in pairs, and write all records to the output file.
- while (record1.qName != "*" || record2.qName != "*")
- {
- while ((compare_qName(record2.qName, record1.qName) < 0 || record1.qName == "*") && record2.qName != "*")
- {
- writeRecord(outStream, record2);
- if (!atEnd(remappedStream)) readRecordAndCorrectRIds(record2, remappedStream, contigNamesCache(bamContextDep));
- else record2.qName = "*";
- }
-
- bool incr1 = false;
- while (record1.qName == record2.qName && record2.qName != "*")
- {
- incr1 = true;
- setMates(record1, record2);
- writeRecord(outStream, record1);
- writeRecord(outStream, record2);
- if (!atEnd(remappedStream)) readRecordAndCorrectRIds(record2, remappedStream, contigNamesCache(bamContextDep));
- else record2.qName = "*";
- }
- if (incr1)
- {
- if (!atEnd(nonRefStream)) readRecordAndCorrectRIds(record1, nonRefStream, contigNamesCache(bamContextDep));
- else record1.qName = "*";
- }
-
- while ((compare_qName(record1.qName, record2.qName) < 0 || record2.qName == "*") && record1.qName != "*")
- {
- writeRecord(outStream, record1);
- if (!atEnd(nonRefStream)) readRecordAndCorrectRIds(record1, nonRefStream, contigNamesCache(bamContextDep));
- else record1.qName = "*";
- }
- }
-
- return 0;
-}
-
-// ==========================================================================
-// Function sickle_filtering()
-// ==========================================================================
-
-inline bool
-sickle_filtering(Triple<CharString> & filteredFiles,
- Triple<CharString> & fastqFiles,
- CharString & workingDirectory)
-{
- std::stringstream cmd;
-
- std::ostringstream msg;
- msg << "Filtering fastq files using " << SICKLE ;
- printStatus(msg);
-
- cmd.str("");
- cmd << SICKLE << " pe -q 20 -l 60 -x -n -t sanger -f" << fastqFiles.i1 << " -r " << fastqFiles.i2;
- cmd << " -o " << filteredFiles.i1 << " -p " << filteredFiles.i2 << " -s " << filteredFiles.i3;
- if (system(cmd.str().c_str()) != 0) // runs sickle on paired end reads
- {
- std::cerr << "ERROR while filtering " << fastqFiles.i1 << " and " << fastqFiles.i2;
- std::cerr << " using " << SICKLE << std::endl;
- return 1;
- }
-
- CharString singleFiltered2 = getFileName(workingDirectory, "filtered.single2.fastq");
-
- cmd.str("");
- cmd << SICKLE << " se -q 20 -l 60 -x -n -t sanger -f " << fastqFiles.i3 << " -o " << singleFiltered2;
- if (system(cmd.str().c_str()) != 0) // runs sickle on single end reads
- {
- std::cerr << "ERROR while filtering " << fastqFiles.i3 << " using " << SICKLE << std::endl;
- return 1;
- }
-
- cmd.str("");
- cmd << "cat " << singleFiltered2 << " >> " << filteredFiles.i3;
- if (system(cmd.str().c_str()) != 0) // merges the fastq files of single end reads.
- {
- std::cerr << "ERROR while concatenating " << singleFiltered2 << " to " << filteredFiles.i3 << std::endl;
- return 1;
- }
-
- remove(toCString(singleFiltered2));
-
- return 0;
-}
-
-// ==========================================================================
-// Function velvet_assembly()
-// ==========================================================================
-
-inline bool
-velvet_assembly(Triple<CharString> & filteredFiles, Triple<CharString> & filteredMPFiles, CharString & assemblyDirectory, unsigned kmerLength, bool matepair)
-{
- std::stringstream cmd;
-
- std::ostringstream msg;
- msg << "Preparing assembly of unmapped reads from filtered fastq files using " << VELVETH;
- printStatus(msg);
-
- cmd.str("");
- cmd << VELVETH << " " << assemblyDirectory << " " << kmerLength << " -short -fastq " << filteredFiles.i3;
- cmd << " -shortPaired -fastq -separate " << filteredFiles.i1 << " " << filteredFiles.i2;
- if (matepair) {
- cmd << " -shortPaired2 -fastq -separate " << filteredMPFiles.i1 << " " << filteredMPFiles.i2;
- }
-
- if (system(cmd.str().c_str()) != 0) // prepares velvet assembly, use k=47 for longer contigs
- {
- std::cerr << "ERROR while preparing assembly with " << VELVETH << " of ";
- std::cerr << filteredFiles.i3 << ", " << filteredFiles.i1 << ", and " << filteredFiles.i2 << std::endl;
- if (matepair) {
- std::cerr << "and matepair files " << filteredMPFiles.i1 << " and " << filteredMPFiles.i2 << std::endl;
- }
- return 1;
- }
-
- msg.str("");
- msg << "Assembling unmapped reads from filtered fastq files using " << VELVETG;
- printStatus(msg);
-
- cmd.str("");
- cmd << VELVETG << " " << assemblyDirectory << " -exp_cov auto -cov_cutoff 2 -max_coverage 100 -scaffolding no";
- if (matepair) {
- cmd << " -shortMatePaired2 yes";
- }
-
- if (system(cmd.str().c_str()) != 0) // runs the velvet graph part
- {
- std::cerr << "ERROR while assembling " << assemblyDirectory << " with " << VELVETG << std::endl;
- return 1;
- }
-
- return 0;
-}
-
-
-// ==========================================================================
-// Function velvet_assembly()
-// ==========================================================================
-
-inline bool minia_assembly(Triple<CharString> & filteredFiles, CharString & assemblyDirectory, const unsigned threads) {
- std::stringstream cmd;
-
- std::ostringstream msg;
- msg << "Preparing assembly of unmapped reads from filtered fastq files using " << MINIA;
- printStatus(msg);
-
- cmd.str("");
- cmd << MINIA << " --nb-cores " << threads;
- cmd << " -1 " << filteredFiles.i1 << " -2 " << filteredFiles.i2 << " -s " << filteredFiles.i3;
- cmd << " -o " << assemblyDirectory << "/assembly";
- cmd << " --no-scaffolding";
-
- if (system(cmd.str().c_str()) != 0) // prepares minia assembly, k is automatically iteratively increased
- {
- std::cerr << "ERROR while preparing assembly with " << MINIA << " of ";
- std::cerr << filteredFiles.i3 << ", " << filteredFiles.i1 << ", and " << filteredFiles.i2 << std::endl;
- return 1;
- }
-
- return 0;
-}
-
-
-// ==========================================================================
-// Function popins_assemble()
-// ==========================================================================
-
-int popins2_assemble(int argc, char const ** argv)
-{
- std::ostringstream msg;
-
- // Parse the command line to get option values.
- Options options;
- ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
- if (res != ArgumentParser::PARSE_OK)
- return res;
-
- // Retrieve the sample ID from the first read group listed in BAM file header.
- if (options.sampleID == "" && retrieveSampleID(options.sampleID, options.mappingFile) == 1)
- return 7;
-
- // Create working directory if it does not exist.
- CharString workingDirectory = getFileName(options.prefix, options.sampleID);
- if (mkdir(toCString(workingDirectory), 0755) == 0)
- {
- msg.str("");
- msg << "Working directory created at " << workingDirectory;
- printStatus(msg);
- }
-
- SampleInfo info = initSampleInfo(options.mappingFile, options.sampleID, options.adapters);
-
- float as_factor = options.alignment_score_factor;
-
- CharString matesBam = getFileName(workingDirectory, "mates.bam");
- CharString nonRefBamTemp = getFileName(workingDirectory, "non_ref_tmp.bam");
- CharString nonRefBam = getFileName(workingDirectory, "non_ref.bam");
-
- CharString fastqFirst = getFileName(workingDirectory, "paired.1.fastq");
- CharString fastqSecond = getFileName(workingDirectory, "paired.2.fastq");
- CharString fastqSingle = getFileName(workingDirectory, "single.fastq");
- Triple<CharString> fastqFiles = Triple<CharString>(fastqFirst, fastqSecond, fastqSingle);
-
- CharString firstFiltered = getFileName(workingDirectory, "filtered.paired.1.fastq");
- CharString secondFiltered = getFileName(workingDirectory, "filtered.paired.2.fastq");
- CharString singleFiltered = getFileName(workingDirectory, "filtered.single.fastq");
- Triple<CharString> filteredFiles(firstFiltered, secondFiltered, singleFiltered);
-
- // MP handling
- CharString matesMPBam = getFileName(workingDirectory, "MP.mates.bam");
- CharString nonRefBamMPTemp = getFileName(workingDirectory, "MP.non_ref_tmp.bam");
- CharString nonRefMPBam = getFileName(workingDirectory, "MP.non_ref.bam");
-
- CharString fastqMPFirst = getFileName(workingDirectory, "MP.paired.1.fastq");
- CharString fastqMPSecond = getFileName(workingDirectory, "MP.paired.2.fastq");
- CharString fastqMPSingle = getFileName(workingDirectory, "MP.single.fastq");
- Triple<CharString> fastqMPFiles = Triple<CharString>(fastqMPFirst, fastqMPSecond, fastqMPSingle);
-
- // check if files already exits
- std::fstream stream(toCString(fastqFirst));
- if (!stream.is_open())
- {
- msg.str("");
- msg << "Cropping unmapped reads from " << options.mappingFile;
- printStatus(msg);
-
- // Crop unmapped reads and reads with unreliable mappings from the input bam file.
- if (options.adapters == "HiSeqX")
- {
- if (crop_unmapped(info.avg_cov, fastqFiles, matesBam, options.mappingFile, options.humanSeqs, HiSeqXAdapters(), as_factor) != 0)
- return 7;
- }
- else if (options.adapters == "HiSeq")
- {
- if (crop_unmapped(info.avg_cov, fastqFiles, matesBam, options.mappingFile, options.humanSeqs, HiSeqAdapters(), as_factor) != 0)
- return 7;
- }
- else
- {
- if (crop_unmapped(info.avg_cov, fastqFiles, matesBam, options.mappingFile, options.humanSeqs, NoAdapters(), as_factor) != 0)
- return 7;
- }
-
- CharString sampleInfoFile = getFileName(workingDirectory, "POPINS_SAMPLE_INFO");
- writeSampleInfo(info, sampleInfoFile);
-
- msg.str("");
- msg << "Sample info written to \'" << sampleInfoFile << "\'.";
- printStatus(msg);
-
-
- }
-
- CharString firstMPFiltered = getFileName(workingDirectory, "MP.filtered.paired.1.fastq");
- CharString secondMPFiltered = getFileName(workingDirectory, "MP.filtered.paired.2.fastq");
- CharString singleMPFiltered = getFileName(workingDirectory, "MP.filtered.single.fastq");
-
- Triple<CharString> filteredMPFiles(firstMPFiltered, secondMPFiltered, singleMPFiltered);
-
- if (options.matepairFile != ""){
- if (sickle_filtering(filteredMPFiles,fastqMPFiles, workingDirectory) != 0)
- return 7;
- }
-
-
-
-
- if (!options.skip_assembly){ // if you use the multik module or an independent assembler you might want to skip the assembly here
-
- CharString assemblyDirectory = getFileName(workingDirectory, "assembly");
- if (options.use_velvet){
-
- // Assembly with velvet.
- if (velvet_assembly(filteredFiles, filteredMPFiles, assemblyDirectory, options.kmerLength, options.matepairFile != "") != 0)
- return 7;
-
- if (options.matepairFile == ""){
- remove(toCString(firstMPFiltered));
- remove(toCString(secondMPFiltered));
- remove(toCString(singleMPFiltered));
- }
-
- // Copy contigs file to workingDirectory and remove assembly directory.
- CharString contigFileAssembly = getFileName(assemblyDirectory, "contigs.fa");
- CharString contigFile = getFileName(workingDirectory, "contigs.fa");
- std::ifstream src(toCString(contigFileAssembly), std::ios::binary);
- std::ofstream dst(toCString(contigFile), std::ios::binary);
- dst << src.rdbuf();
- src.close();
- dst.close();
- removeAssemblyDirectory(assemblyDirectory);
- }
- else{
-
- // Assembly with minia. (default)
- if (mkdir(toCString(assemblyDirectory), 0755) == 0){ // in contrast to Velvet, minia does not create a missing directory at runtime
- msg.str("");
- msg << "Assembly directory created at " << workingDirectory;
- printStatus(msg);
- }
- if (minia_assembly(filteredFiles, assemblyDirectory, options.threads) != 0)
- return 7;
-
- // Copy contigs file to workingDirectory
- CharString contigFileAssembly = getFileName(assemblyDirectory, "assembly_final.contigs.fa");
- CharString contigFile = getFileName(workingDirectory, "assembly_final.contigs.fa");
- //cout << "assemblyDirectory: " << assemblyDirectory << endl;
- //cout << "workingDirectory: " << workingDirectory << endl;
- std::ifstream src(toCString(contigFileAssembly), std::ios::binary);
- std::ofstream dst(toCString(contigFile), std::ios::binary);
- dst << src.rdbuf();
- src.close();
- dst.close();
-
- // remove assembly directory
- std::stringstream cmd;
- cmd.str("");
- cmd << "rm -rf " << assemblyDirectory;
- system(cmd.str().c_str());
- }
- }
-
-
- remove(toCString(firstFiltered));
- remove(toCString(secondFiltered));
- remove(toCString(singleFiltered));
-
- return res;
-
-}
-
-#endif // #ifndef POPINS_ASSEMBLE_H_
-
-
-/*
-#try deleting part of the functions
-#rename functions
-#sickle (try to get rid)
-#conda package (help with the installation)
-*/
\ No newline at end of file
diff --git a/src/popins2_assemble_old.h b/src/popins2_assemble_old.h
deleted file mode 100644
index 2e23a171f1e812bb3458359d46e45b0d3c324296..0000000000000000000000000000000000000000
--- a/src/popins2_assemble_old.h
+++ /dev/null
@@ -1,792 +0,0 @@
-#include <sstream>
-#include <cerrno>
-
-#include <seqan/file.h>
-#include <seqan/sequence.h>
-
-#include "util.h"
-#include "argument_parsing.h"
-#include "crop_unmapped.h"
-
-#ifndef POPINS_ASSEMBLE_H_
-#define POPINS_ASSEMBLE_H_
-
-using namespace seqan;
-
-// ==========================================================================
-
-inline void
-removeAssemblyDirectory(CharString & path)
-{
- removeFile(path, "contigs.fa");
- removeFile(path, "Graph2");
- removeFile(path, "LastGraph");
- removeFile(path, "Log");
- removeFile(path, "PreGraph");
- removeFile(path, "Roadmaps");
- removeFile(path, "Sequences");
- removeFile(path, "stats.txt");
- remove(toCString(path));
-}
-
-bool retrieveSampleID(CharString & sampleID, CharString & mappingBam)
-{
- BamFileIn inStream(toCString(mappingBam));
-
- BamHeader header;
- readHeader(header, inStream);
-
- for (unsigned i = 0; i < length(header); ++i)
- {
- if (header[i].type != BamHeaderRecordType::BAM_HEADER_READ_GROUP)
- continue;
-
- for (unsigned j = 0; j < length(header[i].tags); ++j)
- {
- if (header[i].tags[j].i1 != "SM")
- continue;
-
- sampleID = header[i].tags[j].i2;
- return 0;
- }
- }
- std::cerr << "ERROR: Could not find sample ID in BAM file header." << std::endl;
- return 1;
-}
-
-// ==========================================================================
-// Function remapping()
-// ==========================================================================
-
-inline int remapping(Triple<CharString> & fastqFilesTemp,
- Triple<CharString> & fastqFiles,
- CharString const & referenceFile,
- CharString const & workingDir,
- unsigned humanSeqs,
- unsigned threads,
- CharString & memory,
- CharString & prefix,
- float as_factor)
-{
- std::stringstream cmd;
-
- CharString f1 = prefix;
- f1 += "remapped.sam";
- CharString remappedSam = getFileName(workingDir, f1);
-
- CharString f2 = prefix;
- f2 += "remapped.bam";
- CharString remappedBam = getFileName(workingDir, f2);
-
- CharString f3 = prefix;
- f3 += "remapped.bam.bai";
- CharString remappedBai = getFileName(workingDir, f3);
-
- CharString f4 = prefix;
- f4 += "remapped_unsorted.bam";
- CharString remappedUnsortedBam = getFileName(workingDir, f4);
-
- std::ostringstream msg;
- msg << "Remapping unmapped reads using " << BWA;
- printStatus(msg);
-
- // Run BWA on unmapped reads (pairs).
- cmd.str("");
- cmd << BWA << " mem -t " << threads << " " << referenceFile << " " << fastqFilesTemp.i1 << " " << fastqFilesTemp.i2 << " > " << remappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFilesTemp.i1 << " and " << fastqFilesTemp.i2 << std::endl;
- return 1;
- }
-
- remove(toCString(fastqFilesTemp.i1));
- remove(toCString(fastqFilesTemp.i2));
-
- // Run BWA on unmapped reads (single end).
- cmd.str("");
- cmd << BWA << " mem -t " << threads << " " << referenceFile << " " << fastqFilesTemp.i3 << " | awk '$1 !~ /@/' >> " << remappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFilesTemp.i3 << std::endl;
- return 1;
- }
-
- remove(toCString(fastqFilesTemp.i3));
-
- msg.str("");
- msg << "Converting BWA output " << remappedSam << " to bam format.";
- printStatus(msg);
-
- // Convert BWA output to bam.
- cmd.str("");
- cmd << SAMTOOLS << " view -S -h -b " << remappedSam << " > " << remappedUnsortedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while converting BWA output " << remappedSam << " to bam." << std::endl;
- return 1;
- }
- remove(toCString(remappedSam));
-
- msg.str("");
- msg << "Sorting " << remappedUnsortedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort bam file.
- cmd.str("");
- cmd << SAMTOOLS << " sort -@ " << threads << " -m " << memory << " -o " << remappedBam << " " << remappedUnsortedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting BWA output " << remappedUnsortedBam << std::endl;
- return 1;
- }
-
- msg.str("");
- msg << "Indexing " << remappedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Index bam file.
- cmd.str("");
- cmd << SAMTOOLS << " index " << remappedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while indexing BWA output " << remappedBam << std::endl;
- return 1;
- }
-
- msg.str("");
- msg << "Cropping unmapped reads from " << remappedBam;
- printStatus(msg);
-
- // Crop unmapped and create bam file of remapping.
- if (crop_unmapped(fastqFiles, remappedUnsortedBam, remappedBam, humanSeqs, NoAdapters(), as_factor) != 0)
- return 1;
- remove(toCString(remappedBai));
-
- msg.str("");
- msg << "Sorting " << remappedUnsortedBam << " by read name using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/remapped.bam by read name.
- cmd.str("");
- cmd << SAMTOOLS << " sort -n -@ " << threads << " -m " << memory << " -o " << remappedBam << " " << remappedUnsortedBam << " ";
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << remappedUnsortedBam << std::endl;
- return 1;
- }
-
- remove(toCString(remappedUnsortedBam));
-
- return 0;
-}
-
-// ==========================================================================
-
-inline void setMates(BamAlignmentRecord & record1, BamAlignmentRecord & record2) {
- SEQAN_ASSERT(!hasFlagFirst(record1) || !hasFlagFirst(record2));
- SEQAN_ASSERT(!hasFlagLast(record1) || !hasFlagLast(record2));
-
- // Set the next ref id.
- record1.rNextId = record2.rID;
- record2.rNextId = record1.rID;
-
- // Set the next ref pos.
- record1.pNext = record2.beginPos;
- record2.pNext = record1.beginPos;
-
- // Fix the next unmapped flag.
- if (hasFlagUnmapped(record2)) record1.flag |= BAM_FLAG_NEXT_UNMAPPED;
- else record1.flag &= ~BAM_FLAG_NEXT_UNMAPPED;
- if (hasFlagUnmapped(record1)) record2.flag |= BAM_FLAG_NEXT_UNMAPPED;
- else record2.flag &= ~BAM_FLAG_NEXT_UNMAPPED;
-
- // Fix the next reversed flag.
- if (hasFlagRC(record2)) record1.flag |= BAM_FLAG_NEXT_RC;
- else record1.flag &= ~BAM_FLAG_NEXT_RC;
- if (hasFlagRC(record1)) record2.flag |= BAM_FLAG_NEXT_RC;
- else record2.flag &= ~BAM_FLAG_NEXT_RC;
-
- // Fix first/second in pair flags.
- if (hasFlagFirst(record1)) record2.flag |= BAM_FLAG_LAST;
- if (hasFlagFirst(record2)) record1.flag |= BAM_FLAG_LAST;
- if (hasFlagLast(record1)) record2.flag |= BAM_FLAG_FIRST;
- if (hasFlagLast(record2)) record1.flag |= BAM_FLAG_FIRST;
-
- // Set flag paired.
- record1.flag |= BAM_FLAG_MULTIPLE;
- record2.flag |= BAM_FLAG_MULTIPLE;
-}
-
-// ==========================================================================
-
-// Correct the reference ids of a BamAlignmentRecord for the concatenated header.
-template<typename TNameStore>
-inline void readRecordAndCorrectRIds(BamAlignmentRecord & record, BamFileIn & stream, NameStoreCache<TNameStore> & nameStoreCache){
- readRecord(record, stream);
-
- if (record.rID != BamAlignmentRecord::INVALID_REFID)
- {
- CharString rName = contigNames(context(stream))[record.rID];
- getIdByName(record.rID, nameStoreCache, rName);
- }
- if (record.rNextId != BamAlignmentRecord::INVALID_REFID)
- {
- CharString rNextName = contigNames(context(stream))[record.rNextId];
- getIdByName(record.rNextId, nameStoreCache, rNextName);
- }
-}
-
-// ==========================================================================
-
-inline void mergeHeaders(BamHeader & header, FormattedFileContext<BamFileOut, Owner<> >::Type & context, BamFileIn & stream1, BamFileIn & stream2){
- StringSet<CharString> contigNames;
- NameStoreCache<StringSet<CharString> > nameStoreCache;
- String<int32_t> contigLengths;
-
- // Read and append the two headers. Remove duplicate entries.
- readHeader(header, stream1);
- BamHeader header2;
- readHeader(header2, stream2);
- for (unsigned i = 0; i < length(header2); ++i)
- {
- if (header2[i].type != BAM_HEADER_FIRST)
- appendValue(header, header2[i]);
- }
- std::stable_sort(begin(header, Standard()), end(header, Standard()), BamHeaderRecordTypeLess());
-
- // Fill sequence names into nameStoreCache.
- for (unsigned i = 0; i < length(header); ++i)
- {
- if (header[i].type == BAM_HEADER_REFERENCE)
- {
- CharString name, len;
- for (unsigned j = 0; j < length(header[i].tags); ++j)
- {
- if (header[i].tags[j].i1 == "SN")
- name = header[i].tags[j].i2;
- else if (header[i].tags[j].i1 == "LN")
- len = header[i].tags[j].i2;
- }
- appendName(context._contigNamesCache, name);
- int32_t l;
- lexicalCast<int32_t>(l, len);
- appendValue(context._contigLengths, l);
- }
- }
-}
-
-// ==========================================================================
-
-// This function is adapted from samtools code (fuction strnum_cmp in bam_sort.c) to ensure the exact same sort order.
-int
-compare_qName(CharString & nameA, CharString & nameB)
-{
- const char * _a = toCString(nameA);
- const char * _b = toCString(nameB);
- const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
- const unsigned char *pa = a, *pb = b;
- while (*pa && *pb) {
- if (isdigit(*pa) && isdigit(*pb)) {
- while (*pa == '0') ++pa;
- while (*pb == '0') ++pb;
- while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
- if (isdigit(*pa) && isdigit(*pb)) {
- int i = 0;
- while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
- return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
- } else if (isdigit(*pa)) return 1;
- else if (isdigit(*pb)) return -1;
- else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
- } else {
- if (*pa != *pb) return (int)*pa - (int)*pb;
- ++pa; ++pb;
- }
- }
- return *pa? 1 : *pb? -1 : 0;
-}
-
-// ==========================================================================
-// Function merge_and_set_mate()
-// ==========================================================================
-
-bool
-merge_and_set_mate(CharString &mergedBam, unsigned &nonContigSeqs, CharString &nonRefBam, CharString &remappedBam)
-{
- std::ostringstream msg;
- msg << "Merging bam files " << nonRefBam << " and " << remappedBam;
- printStatus(msg);
-
- // Open the two input streams (can read SAM and BAM files).
- BamFileIn nonRefStream(toCString(nonRefBam));
- BamFileIn remappedStream(toCString(remappedBam));
-
- printStatus(" - merging headers...");
-
- // Prepare a header for the output file.
- BamHeader outHeader;
- FormattedFileContext<BamFileOut, Owner<> >::Type bamContext;
- mergeHeaders(outHeader, bamContext, nonRefStream, remappedStream);
-
- printStatus(" - writing header...");
-
- // Open the output stream and write the header.
- FormattedFileContext<BamFileOut, Dependent<> >::Type bamContextDep(bamContext);
- BamFileOut outStream(bamContextDep, toCString(mergedBam));
- writeHeader(outStream, outHeader);
-
- nonContigSeqs = length(contigNames(context(nonRefStream)));
-
- printStatus(" - merging read records...");
-
- // Read the first record from each input file. Correct ids in records from remappedStreams for new header.
- BamAlignmentRecord record1, record2;
- if (!atEnd(nonRefStream)) readRecordAndCorrectRIds(record1, nonRefStream, contigNamesCache(bamContextDep));
- else record1.qName = "*";
- if (!atEnd(remappedStream)) readRecordAndCorrectRIds(record2, remappedStream, contigNamesCache(bamContextDep));
- else record2.qName = "*";
-
- // Iterate both input files, set mate positions in pairs, and write all records to the output file.
- while (record1.qName != "*" || record2.qName != "*")
- {
- while ((compare_qName(record2.qName, record1.qName) < 0 || record1.qName == "*") && record2.qName != "*")
- {
- writeRecord(outStream, record2);
- if (!atEnd(remappedStream)) readRecordAndCorrectRIds(record2, remappedStream, contigNamesCache(bamContextDep));
- else record2.qName = "*";
- }
-
- bool incr1 = false;
- while (record1.qName == record2.qName && record2.qName != "*")
- {
- incr1 = true;
- setMates(record1, record2);
- writeRecord(outStream, record1);
- writeRecord(outStream, record2);
- if (!atEnd(remappedStream)) readRecordAndCorrectRIds(record2, remappedStream, contigNamesCache(bamContextDep));
- else record2.qName = "*";
- }
- if (incr1)
- {
- if (!atEnd(nonRefStream)) readRecordAndCorrectRIds(record1, nonRefStream, contigNamesCache(bamContextDep));
- else record1.qName = "*";
- }
-
- while ((compare_qName(record1.qName, record2.qName) < 0 || record2.qName == "*") && record1.qName != "*")
- {
- writeRecord(outStream, record1);
- if (!atEnd(nonRefStream)) readRecordAndCorrectRIds(record1, nonRefStream, contigNamesCache(bamContextDep));
- else record1.qName = "*";
- }
- }
-
- return 0;
-}
-
-// ==========================================================================
-// Function sickle_filtering()
-// ==========================================================================
-
-inline bool
-sickle_filtering(Triple<CharString> & filteredFiles,
- Triple<CharString> & fastqFiles,
- CharString & workingDirectory)
-{
- std::stringstream cmd;
-
- std::ostringstream msg;
- msg << "Filtering fastq files using " << SICKLE ;
- printStatus(msg);
-
- cmd.str("");
- cmd << SICKLE << " pe -q 20 -l 60 -x -n -t sanger -f" << fastqFiles.i1 << " -r " << fastqFiles.i2;
- cmd << " -o " << filteredFiles.i1 << " -p " << filteredFiles.i2 << " -s " << filteredFiles.i3;
- if (system(cmd.str().c_str()) != 0) // runs sickle on paired end reads
- {
- std::cerr << "ERROR while filtering " << fastqFiles.i1 << " and " << fastqFiles.i2;
- std::cerr << " using " << SICKLE << std::endl;
- return 1;
- }
-
- CharString singleFiltered2 = getFileName(workingDirectory, "filtered.single2.fastq");
-
- cmd.str("");
- cmd << SICKLE << " se -q 20 -l 60 -x -n -t sanger -f " << fastqFiles.i3 << " -o " << singleFiltered2;
- if (system(cmd.str().c_str()) != 0) // runs sickle on single end reads
- {
- std::cerr << "ERROR while filtering " << fastqFiles.i3 << " using " << SICKLE << std::endl;
- return 1;
- }
-
- cmd.str("");
- cmd << "cat " << singleFiltered2 << " >> " << filteredFiles.i3;
- if (system(cmd.str().c_str()) != 0) // merges the fastq files of single end reads.
- {
- std::cerr << "ERROR while concatenating " << singleFiltered2 << " to " << filteredFiles.i3 << std::endl;
- return 1;
- }
-
- remove(toCString(singleFiltered2));
-
- return 0;
-}
-
-// ==========================================================================
-// Function velvet_assembly()
-// ==========================================================================
-
-inline bool
-velvet_assembly(Triple<CharString> & filteredFiles, Triple<CharString> & filteredMPFiles, CharString & assemblyDirectory, unsigned kmerLength, bool matepair)
-{
- std::stringstream cmd;
-
- std::ostringstream msg;
- msg << "Preparing assembly of unmapped reads from filtered fastq files using " << VELVETH;
- printStatus(msg);
-
- cmd.str("");
- cmd << VELVETH << " " << assemblyDirectory << " " << kmerLength << " -short -fastq " << filteredFiles.i3;
- cmd << " -shortPaired -fastq -separate " << filteredFiles.i1 << " " << filteredFiles.i2;
- if (matepair) {
- cmd << " -shortPaired2 -fastq -separate " << filteredMPFiles.i1 << " " << filteredMPFiles.i2;
- }
-
- if (system(cmd.str().c_str()) != 0) // prepares velvet assembly, use k=47 for longer contigs
- {
- std::cerr << "ERROR while preparing assembly with " << VELVETH << " of ";
- std::cerr << filteredFiles.i3 << ", " << filteredFiles.i1 << ", and " << filteredFiles.i2 << std::endl;
- if (matepair) {
- std::cerr << "and matepair files " << filteredMPFiles.i1 << " and " << filteredMPFiles.i2 << std::endl;
- }
- return 1;
- }
-
- msg.str("");
- msg << "Assembling unmapped reads from filtered fastq files using " << VELVETG;
- printStatus(msg);
-
- cmd.str("");
- cmd << VELVETG << " " << assemblyDirectory << " -exp_cov auto -cov_cutoff 2 -max_coverage 100 -scaffolding no";
- if (matepair) {
- cmd << " -shortMatePaired2 yes";
- }
-
- if (system(cmd.str().c_str()) != 0) // runs the velvet graph part
- {
- std::cerr << "ERROR while assembling " << assemblyDirectory << " with " << VELVETG << std::endl;
- return 1;
- }
-
- return 0;
-}
-
-
-// ==========================================================================
-// Function minia_assembly()
-// ==========================================================================
-
-inline bool minia_assembly(Triple<CharString> & filteredFiles, CharString & assemblyDirectory, const unsigned threads) {
- std::stringstream cmd;
-
- std::ostringstream msg;
- msg << "Preparing assembly of unmapped reads from filtered fastq files using " << MINIA;
- printStatus(msg);
-
- cmd.str("");
- cmd << MINIA << " --nb-cores " << threads;
- cmd << " -1 " << filteredFiles.i1 << " -2 " << filteredFiles.i2 << " -s " << filteredFiles.i3;
- cmd << " -o " << assemblyDirectory << "/assembly";
- cmd << " --no-scaffolding";
-
- if (system(cmd.str().c_str()) != 0) // prepares minia assembly, k is automatically iteratively increased
- {
- std::cerr << "ERROR while preparing assembly with " << MINIA << " of ";
- std::cerr << filteredFiles.i3 << ", " << filteredFiles.i1 << ", and " << filteredFiles.i2 << std::endl;
- return 1;
- }
-
- return 0;
-}
-
-
-// ==========================================================================
-// Function popins_assemble()
-// ==========================================================================
-
-int popins2_assemble(int argc, char const ** argv)
-{
- std::ostringstream msg;
-
- // Parse the command line to get option values.
- AssemblyOptions options;
- ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
- if (res != ArgumentParser::PARSE_OK)
- return res;
-
- // Retrieve the sample ID from the first read group listed in BAM file header.
- if (options.sampleID == "" && retrieveSampleID(options.sampleID, options.mappingFile) == 1)
- return 7;
-
- // Create working directory if it does not exist.
- CharString workingDirectory = getFileName(options.prefix, options.sampleID);
- if (mkdir(toCString(workingDirectory), 0755) == 0)
- {
- msg.str("");
- msg << "Working directory created at " << workingDirectory;
- printStatus(msg);
- }
-
- SampleInfo info = initSampleInfo(options.mappingFile, options.sampleID, options.adapters);
-
- float as_factor = options.alignment_score_factor;
-
- CharString matesBam = getFileName(workingDirectory, "mates.bam");
- CharString nonRefBamTemp = getFileName(workingDirectory, "non_ref_tmp.bam");
- CharString nonRefBam = getFileName(workingDirectory, "non_ref.bam");
-
- CharString fastqFirst = getFileName(workingDirectory, "paired.1.fastq");
- CharString fastqSecond = getFileName(workingDirectory, "paired.2.fastq");
- CharString fastqSingle = getFileName(workingDirectory, "single.fastq");
- Triple<CharString> fastqFiles = Triple<CharString>(fastqFirst, fastqSecond, fastqSingle);
-
- // check if files already exits
- std::fstream stream(toCString(fastqFirst));
- if (!stream.is_open())
- {
- msg.str("");
- msg << "Cropping unmapped reads from " << options.mappingFile;
- printStatus(msg);
-
- // Crop unmapped reads and reads with unreliable mappings from the input bam file.
- if (options.adapters == "HiSeqX")
- {
- if (crop_unmapped(info.avg_cov, fastqFiles, matesBam, options.mappingFile, options.humanSeqs, HiSeqXAdapters(), as_factor) != 0)
- return 7;
- }
- else if (options.adapters == "HiSeq")
- {
- if (crop_unmapped(info.avg_cov, fastqFiles, matesBam, options.mappingFile, options.humanSeqs, HiSeqAdapters(), as_factor) != 0)
- return 7;
- }
- else
- {
- if (crop_unmapped(info.avg_cov, fastqFiles, matesBam, options.mappingFile, options.humanSeqs, NoAdapters(), as_factor) != 0)
- return 7;
- }
-
- CharString sampleInfoFile = getFileName(workingDirectory, "POPINS_SAMPLE_INFO");
- writeSampleInfo(info, sampleInfoFile);
-
- msg.str("");
- msg << "Sample info written to \'" << sampleInfoFile << "\'.";
- printStatus(msg);
-
- msg.str("");
- msg << "Sorting " << matesBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/mates.bam by read name.
- std::stringstream cmd;
- if (options.referenceFile != "")
- cmd << SAMTOOLS << " sort -n -@ " << options.threads << " -m " << options.memory << " -o " << nonRefBamTemp << " " << matesBam;
- else
- cmd << SAMTOOLS << " sort -n -@ " << options.threads << " -m " << options.memory << " -o " << nonRefBam << " " << matesBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << matesBam << std::endl;
- return 7;
- }
-
- remove(toCString(matesBam));
-
- // Remapping of unmapped with bwa if a fasta reference is given.
- if (options.referenceFile != "")
- {
- Triple<CharString> fastqFilesTemp = fastqFiles;
- fastqFiles = Triple<CharString>(fastqFirst, fastqSecond, fastqSingle);
-
- // Align with bwa, update fastq files of unaligned reads, and sort remaining bam records by read name.
- CharString remappedBam = getFileName(workingDirectory, "remapped.bam");
- CharString prefix = "";
- if (remapping(fastqFilesTemp, fastqFiles, options.referenceFile, workingDirectory,
- options.humanSeqs, options.threads, options.memory, prefix, as_factor) != 0)
- return 7;
-
- // Set the mate's location and merge non_ref.bam and remapped.bam into a single file.
- unsigned nonContigSeqs;
- if (merge_and_set_mate(nonRefBam, nonContigSeqs, nonRefBamTemp, remappedBam) != 0)
- return 7;
- remove(toCString(remappedBam));
- remove(toCString(nonRefBamTemp));
- }
- }
- else
- {
- printStatus("Found files, skipping cropping step.");
- }
-
- CharString firstFiltered = getFileName(workingDirectory, "filtered.paired.1.fastq");
- CharString secondFiltered = getFileName(workingDirectory, "filtered.paired.2.fastq");
- CharString singleFiltered = getFileName(workingDirectory, "filtered.single.fastq");
- Triple<CharString> filteredFiles(firstFiltered, secondFiltered, singleFiltered);
-
- // Quality filtering/trimming with sickle.
- if (sickle_filtering(filteredFiles, fastqFiles, workingDirectory) != 0)
- return 7;
-
- // MP handling
- CharString matesMPBam = getFileName(workingDirectory, "MP.mates.bam");
- CharString nonRefBamMPTemp = getFileName(workingDirectory, "MP.non_ref_tmp.bam");
- CharString nonRefMPBam = getFileName(workingDirectory, "MP.non_ref.bam");
-
- CharString fastqMPFirst = getFileName(workingDirectory, "MP.paired.1.fastq");
- CharString fastqMPSecond = getFileName(workingDirectory, "MP.paired.2.fastq");
- CharString fastqMPSingle = getFileName(workingDirectory, "MP.single.fastq");
- Triple<CharString> fastqMPFiles = Triple<CharString>(fastqMPFirst, fastqMPSecond, fastqMPSingle);
-
- if (options.matepairFile != "")
- {
- // check if MP files already exits
- std::fstream MPstream(toCString(fastqMPFirst));
- if (!MPstream.is_open())
- {
- msg.str("");
- msg << "Cropping unmapped matepair reads from " << options.matepairFile;
- printStatus(msg);
-
- // Crop unmapped reads and reads with unreliable mappings from the input bam file.
- if (options.adapters == "HiSeqX")
- {
- if (crop_unmapped(fastqMPFiles, matesMPBam, options.matepairFile, options.humanSeqs, HiSeqXAdapters(), as_factor) != 0)
- return 7;
- }
- else if (options.adapters == "HiSeq")
- {
- if (crop_unmapped(fastqMPFiles, matesMPBam, options.matepairFile, options.humanSeqs, HiSeqAdapters(), as_factor) != 0)
- return 7;
- }
- else
- {
- if (crop_unmapped(fastqMPFiles, matesMPBam, options.matepairFile, options.humanSeqs, NoAdapters(), as_factor) != 0)
- return 7;
- }
-
- msg.str("");
- msg << "Sorting " << matesMPBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/mates.bam by read name.
- std::stringstream cmd;
- if (options.referenceFile != "")
- cmd << SAMTOOLS << " sort -n -@ " << options.threads << " -m " << options.memory << " -o " << nonRefBamMPTemp << " " << matesMPBam;
- else
- cmd << SAMTOOLS << " sort -n -@ " << options.threads << " -m " << options.memory << " -o " << nonRefMPBam << " " << matesMPBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << matesMPBam << std::endl;
- return 7;
- }
-
- remove(toCString(matesMPBam));
-
- // Remapping of unmapped with bwa if a fasta reference is given.
- if (options.referenceFile != "")
- {
- Triple<CharString> fastqMPFilesTemp = fastqMPFiles;
- fastqMPFiles = Triple<CharString>(fastqMPFirst, fastqMPSecond, fastqMPSingle);
-
- // Align with bwa, update fastq files of unaligned reads, and sort remaining bam records by read name.
- CharString remappedMPBam = getFileName(workingDirectory, "MP.remapped.bam");
- CharString prefix = "MP.";
- if (remapping(fastqMPFilesTemp, fastqMPFiles, options.referenceFile, workingDirectory,
- options.humanSeqs, options.threads, options.memory, prefix, as_factor) != 0)
- return 7;
-
- // Set the mate's location and merge non_ref.bam and remapped.bam into a single file
- unsigned nonContigSeqs;
- if (merge_and_set_mate(nonRefMPBam, nonContigSeqs, nonRefBamMPTemp, remappedMPBam) != 0)
- return 7;
- remove(toCString(remappedMPBam));
- remove(toCString(nonRefBamMPTemp));
- }
- }
- else
- {
- printStatus("Found matepair files, skipping cropping step");
- }
- }
-
-
- CharString firstMPFiltered = getFileName(workingDirectory, "MP.filtered.paired.1.fastq");
- CharString secondMPFiltered = getFileName(workingDirectory, "MP.filtered.paired.2.fastq");
- CharString singleMPFiltered = getFileName(workingDirectory, "MP.filtered.single.fastq");
-
- Triple<CharString> filteredMPFiles(firstMPFiltered, secondMPFiltered, singleMPFiltered);
-
- if (options.matepairFile != ""){
- if (sickle_filtering(filteredMPFiles,fastqMPFiles, workingDirectory) != 0)
- return 7;
- }
-
- if (!options.skip_assembly){ // if you use the multik module or an independent assembler you might want to skip the assembly here
-
- CharString assemblyDirectory = getFileName(workingDirectory, "assembly");
- if (options.use_velvet){
-
- // Assembly with velvet.
- if (velvet_assembly(filteredFiles, filteredMPFiles, assemblyDirectory, options.kmerLength, options.matepairFile != "") != 0)
- return 7;
-
- if (options.matepairFile == ""){
- remove(toCString(firstMPFiltered));
- remove(toCString(secondMPFiltered));
- remove(toCString(singleMPFiltered));
- }
-
- // Copy contigs file to workingDirectory and remove assembly directory.
- CharString contigFileAssembly = getFileName(assemblyDirectory, "contigs.fa");
- CharString contigFile = getFileName(workingDirectory, "contigs.fa");
- std::ifstream src(toCString(contigFileAssembly), std::ios::binary);
- std::ofstream dst(toCString(contigFile), std::ios::binary);
- dst << src.rdbuf();
- src.close();
- dst.close();
- removeAssemblyDirectory(assemblyDirectory);
- }
- else{
-
- // Assembly with minia. (default)
- if (mkdir(toCString(assemblyDirectory), 0755) == 0){ // in contrast to Velvet, minia does not create a missing directory at runtime
- msg.str("");
- msg << "Assembly directory created at " << workingDirectory;
- printStatus(msg);
- }
- if (minia_assembly(filteredFiles, assemblyDirectory, options.threads) != 0)
- return 7;
-
- // Copy contigs file to workingDirectory
- CharString contigFileAssembly = getFileName(assemblyDirectory, "assembly_final.contigs.fa");
- CharString contigFile = getFileName(workingDirectory, "assembly_final.contigs.fa");
- //cout << "assemblyDirectory: " << assemblyDirectory << endl;
- //cout << "workingDirectory: " << workingDirectory << endl;
- std::ifstream src(toCString(contigFileAssembly), std::ios::binary);
- std::ofstream dst(toCString(contigFile), std::ios::binary);
- dst << src.rdbuf();
- src.close();
- dst.close();
-
- // remove assembly directory
- std::stringstream cmd;
- cmd.str("");
- cmd << "rm -rf " << assemblyDirectory;
- system(cmd.str().c_str());
- }
- }
-
- remove(toCString(firstFiltered));
- remove(toCString(secondFiltered));
- remove(toCString(singleFiltered));
-
- return res;
-}
-
-#endif // #ifndef POPINS_ASSEMBLE_H_
diff --git a/src/popins2_merge_and_set_mate.h b/src/popins2_merge_and_set_mate.h
index 2e9b7eb98f1313e359949de9dd4bfc000e567b3d..e6b4345a3fffdfe90d7a6e6505949481ef11ec89 100644
--- a/src/popins2_merge_and_set_mate.h
+++ b/src/popins2_merge_and_set_mate.h
@@ -144,7 +144,7 @@ inline void mergeHeaders(BamHeader & header, FormattedFileContext<BamFileOut, Ow
//std::cout << "[header1] =========================================" << std::endl;
//std::cout << "[list...] ["; printSet(program_ids); std::cout << "]" << std::endl;
CharString PG_ID;
- bool keyFound = getTagValue(PG_ID, "ID", header1[i]);
+ getTagValue(PG_ID, "ID", header1[i]);
const char* C_PG_ID = toCString(PG_ID);
std::string S_PG_ID(C_PG_ID);
//std::cout << "[header1] " << S_PG_ID << std::endl;
@@ -181,7 +181,7 @@ inline void mergeHeaders(BamHeader & header, FormattedFileContext<BamFileOut, Ow
//std::cout << "[header2] =========================================" << std::endl;
//std::cout << "[list...] ["; printSet(program_ids); std::cout << "]" << std::endl;
CharString PG_ID;
- bool keyFound = getTagValue(PG_ID, "ID", header2[i]);
+ getTagValue(PG_ID, "ID", header2[i]);
const char* C_PG_ID = toCString(PG_ID);
std::string S_PG_ID(C_PG_ID);
//std::cout << "[header2] " << S_PG_ID << std::endl;
diff --git a/src/popins2_multik.h b/src/popins2_multik.h
deleted file mode 100644
index 60273780c3a0461cc41e409fe7f8e6ebc1c5b571..0000000000000000000000000000000000000000
--- a/src/popins2_multik.h
+++ /dev/null
@@ -1,312 +0,0 @@
-/**
- * @file src/popins2_multik.h
- * @brief Creating a multi-k-iterative colored compacted de Bruijn Graph.
- * In the past, the multi-k paradigm for de Bruijn Graphs (dBG) has been shown to be a successful
- * method to transform the topology of a dBG for de novo sequence assembly. The multi-k paradigm
- * aims to increase the average unitig length without the fragmentation of large k values.
- * The multik module extends this idea for colored de Bruijn Graphs by maintaining the color
- * awareness in each iteration.
- */
-
-#ifndef POPINS2_MULTIK_H_
-#define POPINS2_MULTIK_H_
-
-#include <bifrost/ColoredCDBG.hpp> // ColoredCDBG
-#include <seqan/seq_io.h> // getAbsolutePath, toCString, readRecords
-#include "util.h" // getFastx, printTimeStatus, getAbsoluteFileName
-#include "argument_parsing.h" // MultikOptions, parseCommandLine, printMultikOptions
-
-using namespace seqan;
-
-
-
-/**
- * Function to convert FASTQ to FASTA.
- * @details This is the seqAn2 way to do this. Converting this with the new C++20 concepts used in
- * seqAn3 is so much more elegant.
- * @param fastq_file is the name of the fastq file to convert to fasta, including its full path
- * @param outpath is a (optional) string to define an output directory for the FASTA.
- * If outpath is "" the FASTA will be written to the current working directory
- * @param fasta_names is a vector reference to store the absolute FASTA filenames in
- * @return bool; 1 if error, 0 else
- */
-inline bool fastq2fasta(const std::string &fastq_file, const std::string &outpath, std::vector<std::string> &fasta_names){
- // read FASTQ
- CharString seqFileName = fastq_file;
- SeqFileIn seqFileIn;
-
- if (!open(seqFileIn, toCString(seqFileName))){
- std::cerr << "ERROR: Could not open FASTQ file to read from.\n";
- return 1;
- }
-
- StringSet<CharString> ids;
- StringSet<Dna5String> seqs;
- StringSet<CharString> quals;
-
- try{
- readRecords(ids, seqs, quals, seqFileIn);
- }
- catch (Exception const & e){
- std::cout << "ERROR: " << e.what() << std::endl;
- return 1;
- }
-
- close(seqFileIn);
- clear(quals); // we don't need them
-
- // get FASTQ filename without path and without file ending
- size_t lastSlashPos = fastq_file.find_last_of("/");
- std::string fname = fastq_file.substr(lastSlashPos+1);
- size_t lastDotPos = fname.find_last_of(".");
- std::string fname_ = fname.substr(0,lastDotPos);
-
- // create FASTA filename
- std::string ofile_name;
- if (strcmp(outpath.c_str(), "") == 0){
- ofile_name = fname_+".fasta";
- }
- else{
- ofile_name = getAbsoluteFileName(outpath, fname_+".fasta");
- }
- fasta_names.push_back(ofile_name);
-
- // write FASTA
- SeqFileOut seqFileOut(ofile_name.c_str());
- if (!open(seqFileOut, ofile_name.c_str())){
- std::cerr << "ERROR: Could not open FASTA file to write into.\n";
- return 1;
- }
-
- try{
- writeRecords(seqFileOut, ids, seqs);
- }
- catch (Exception const & e){
- std::cout << "ERROR: " << e.what() << std::endl;
- return 1;
- }
-
-
- close(seqFileOut);
-
- return 0;
-}
-
-
-/**
- * This function defines the boolean logic to decide if a color for unitig is significant.
- * @param b1, b2, b3 are boolean values to compare
- */
-inline bool logicDecision(const bool b1, const bool b2, const bool b3){
- // true if at least 2 out of 3 are true
- return b1 ? (b2 || b3) : (b2 && b3);
-}
-
-
-/**
- * This function extract the color bits of a kmer position of UnitigColorMap
- * @param ucm is a unitig of the graph
- * @param colorBits is a vector to store the color bits of the kmer
- * @param pos is the position of the kmer in the unitig (ucm)
- */
-inline void getColorBitsOfPosition(const UnitigColorMap<void> &ucm, std::vector<bool> &colorBits, const size_t pos){
- UnitigColorMap<void> kmer;
- UnitigColors* colors;
-
- kmer = ucm.getKmerMapping(pos);
- colors = kmer.getData()->getUnitigColors(kmer);
-
- UnitigColors::const_iterator cit = colors->begin(kmer);
- for (; cit != colors->end(); ++cit)
- colorBits[cit.getColorID()] = true;
-}
-
-
-/**
- * This function defines how to subsample kmers from a unitig.
- * @param ucm is a unitig of the graph
- * @param color_indices is a list of samples the unitig should be added to
- */
-inline void colorProbing(const UnitigColorMap<void> &ucm, std::vector<size_t> &color_indices, const size_t nb_colors){
- // the current approach is to ckeck the unitig colors at three positions: start, middle and end
- // NOTE: finding the end position usually requires strand awareness, but this is not important here
- size_t end = ucm.len - 1;
- size_t mid = floor(end / 2);
-
- std::vector<bool> startColorBits(nb_colors, false);
- std::vector<bool> middleColorBits(nb_colors, false);
- std::vector<bool> endColorBits(nb_colors, false);
-
- getColorBitsOfPosition(ucm, startColorBits, 0);
- getColorBitsOfPosition(ucm, middleColorBits, mid);
- getColorBitsOfPosition(ucm, endColorBits, end);
-
- for (size_t i = 0; i < nb_colors; ++i)
- if (logicDecision(startColorBits[i], middleColorBits[i], endColorBits[i]))
- color_indices.push_back(i);
-}
-
-
-/**
- * Multik main routine.
- * @return 0=success, 1=error
- */
-int popins2_multik(int argc, char const *argv[]){
- // =====================
- // Argument parsing
- // =====================
- MultikOptions mko;
- seqan::ArgumentParser::ParseResult res = parseCommandLine(mko, argc, argv);
- if (res != seqan::ArgumentParser::PARSE_OK){
- if (res == seqan::ArgumentParser::PARSE_HELP)
- return 0;
- cerr << "[popins2 multik] seqan::ArgumentParser::PARSE_ERROR" << endl;
- return 1;
- }
-
- printMultikOptions(mko);
-
- int delta_k = mko.delta_k;
- int k_max = mko.k_max;
-
- std::ostringstream msg;
- msg << "[popins2 multik] Starting ..."; printTimeStatus(msg);
-
- // manage a temporary directory
- if (strcmp(mko.tempPath.c_str(), "") != 0) // if mko.tempPath != ""
- (mkdir(mko.tempPath.c_str(), 0750) == -1) ? cerr << "Error : " << strerror(errno) << endl : cout << "[popins2 multik] Temp directory created.\n";
-
- // read original FASTQ samples
- //std::vector<std::string> samples;
- //getFastx(samples, mko.samplePath);
-
- // create a FASTA at tempDir for every input FASTQ
- std::vector<std::string> temp_fastas;
- bool fastq2fasta_failed = false;
-
- for (auto &sample : mko.inputFiles){
- bool ret = fastq2fasta(sample, mko.tempPath, temp_fastas);
- fastq2fasta_failed = fastq2fasta_failed || ret;
- }
- if (fastq2fasta_failed){
- std::cerr << "[Error] Initial FASTQ to FASTA conversion failed]" << '\n';
- return 1;
- }
-
- (mko.inputFiles).clear();
-
- // =====================
- // Graph options
- // =====================
- CCDBG_Build_opt opt;
- opt.filename_seq_in = temp_fastas;
- opt.deleteIsolated = true;
- opt.clipTips = true;
- opt.useMercyKmers = false;
- opt.prefixFilenameOut = mko.prefixFilenameOut;
- opt.nb_threads = 16;
- opt.outputGFA = true;
- opt.verbose = false;
- opt.k = mko.k_init;
-
- // =====================
- // Multi-k framework
- // =====================
- unsigned k_iter_counter = 0;
- while (opt.k <= k_max) {
- ++k_iter_counter;
- msg << "[popins2 multik] Multi-k iteration "+std::to_string(k_iter_counter)+" using k="+std::to_string(opt.k); printTimeStatus(msg);
-
- ColoredCDBG<> g(opt.k);
-
- msg << "[popins2 multik] Building dBG..."; printTimeStatus(msg);
- g.buildGraph(opt);
-
- msg << "[popins2 multik] Simplifying dBG..."; printTimeStatus(msg);
- g.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose);
-
- msg << "[popins2 multik] Annotating colors..."; printTimeStatus(msg);
- g.buildColors(opt);
-
- opt.k += delta_k;
-
- // exit point
- if (opt.k > k_max){
- msg << "[popins2 multik] Writing "+opt.prefixFilenameOut+".gfa of de Bruijn Graph built with k="+std::to_string(opt.k - delta_k)+"..."; printTimeStatus(msg);
- g.write(opt.prefixFilenameOut, opt.nb_threads, opt.verbose);
- break;
- }
-
- // get sample-unitig assignment
- msg << "[popins2 multik] Get sample-unitig assignment..."; printTimeStatus(msg);
- const size_t nb_colors = g.getNbColors();
- std::unordered_map <std::string, std::vector<unsigned> > unitig_propagation_table;
- std::vector<size_t> color_indices;
- unsigned ucm_index = 0;
-
- for (auto &ucm : g){
- // don't process unitigs of size less than current k, they wouldn't survive the include of the next k iteration anyway
- if (ucm.size < (unsigned)opt.k){
- ++ucm_index;
- continue;
- }
-
- colorProbing(ucm, color_indices, nb_colors);
-
- for (size_t i = 0; i < color_indices.size(); ++i)
- unitig_propagation_table[g.getColorName(i)].push_back(ucm_index);
-
- ++ucm_index;
- color_indices.clear();
- }
-
- // write unitig file per sample
- msg << "[popins2 multik] Adding (k + delta_k)-unitigs to temp FASTAs..."; printTimeStatus(msg);
- for (auto sample = unitig_propagation_table.cbegin(); sample != unitig_propagation_table.cend(); ++sample){
-
- std::ofstream stream(sample->first, std::ofstream::out | std::ofstream::app);
- if (!stream.good())
- {
- std::cerr << "ERROR: Could not open sample file \'" << sample->first << "\' for writing." << std::endl;
- return 1;
- }
-
- // iterators pointing to the unitig ID list of a sample
- std::vector<unsigned>::const_iterator idx = sample->second.cbegin();
- std::vector<unsigned>::const_iterator idx_end = sample->second.cend();
-
- // loop through graph
- unsigned current_ucm_idx = 0;
- for (auto &ucm : g){
-
- if (*idx == current_ucm_idx){
-
- // write unitig to file
- stream << ">unitig_" << std::to_string(current_ucm_idx) << "\n";
- stream << ucm.referenceUnitigToString() << "\n";
-
- ++idx;
-
- if (idx == idx_end)
- break;
- }
-
- current_ucm_idx += 1;
- }
-
- stream.close();
- }
-
- }
-
- // =====================
- // EOF
- // =====================
- msg << "[popins2 multik] Done."; printTimeStatus(msg);
-
- return 0;
-}
-
-
-
-#endif /*POPINS2_MULTIK_H_*/
diff --git a/src/popins2_remapping.h b/src/popins2_remapping.h
deleted file mode 100644
index ffd863923f64c72e0c3b3f193ca840556b4034e8..0000000000000000000000000000000000000000
--- a/src/popins2_remapping.h
+++ /dev/null
@@ -1,165 +0,0 @@
-#include <sstream>
-#include <cerrno>
-
-#include <seqan/file.h>
-#include <seqan/sequence.h>
-
-#include "util.h"
-#include "argument_parsing.h"
-#include "crop_unmapped.h"
-
-#ifndef POPINS2_REMAPPING_H_
-#define POPINS2_REMAPPING_H_
-
-using namespace seqan;
-
-
-// ==========================================================================
-// Function popins2_remapping()
-// could be taken apart in snakemake, only calling external functions(SAMTOOLS/BWA)
-// ==========================================================================
-
-inline int popins2_remapping(int argc, char const ** argv)
-{
- std::stringstream cmd;
- std::ostringstream msg;
-
- RemappingOptions options;
- ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
- if (res != ArgumentParser::PARSE_OK)
- {
- return res;
- }
- // Create working directory if it does not exist.
- CharString workingDirectory = getFileName(options.prefix, options.sampleID);
- if (mkdir(toCString(workingDirectory), 0755) == 0)
- {
- msg.str("");
- msg << "Working directory created at " << workingDirectory;
- printStatus(msg);
- }
-
- CharString fastqFirst = getFileName(workingDirectory, "paired.1.fastq");
- CharString fastqSecond = getFileName(workingDirectory, "paired.2.fastq");
- CharString fastqSingle = getFileName(workingDirectory, "single.fastq");
- Triple<CharString> fastqFiles = Triple<CharString>(fastqFirst, fastqSecond, fastqSingle);
-
- Triple<CharString> fastqFilesTemp = fastqFiles;
-
-
- CharString f1 = options.prefix;
- f1 += "remapped.sam";
- CharString remappedSam = getFileName(options.workingDir, f1);
-
- CharString f2 = options.prefix;
- f2 += "remapped.bam";
- CharString remappedBam = getFileName(options.workingDir, f2);
-
- CharString f3 = options.prefix;
- f3 += "remapped.bam.bai";
- CharString remappedBai = getFileName(options.workingDir, f3);
-
- CharString f4 = options.prefix;
- f4 += "remapped_unsorted.bam";
- CharString remappedUnsortedBam = getFileName(options.workingDir, f4);
-
-
- msg << "Remapping unmapped reads using " << BWA;
- printStatus(msg);
-
-
-
- // Run BWA on unmapped reads (pairs).
- cmd.str("");
- cmd << BWA << " mem -t " << options.threads << " " << options.referenceFile << " " << fastqFilesTemp.i1 << " " << fastqFilesTemp.i2 << " > " << remappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFilesTemp.i1 << " and " << fastqFilesTemp.i2 << std::endl;
- return 1;
- }
-
- remove(toCString(fastqFilesTemp.i1));
- remove(toCString(fastqFilesTemp.i2));
-
- // Run BWA on unmapped reads (single end).
- cmd.str("");
- cmd << BWA << " mem -t " << options.threads << " " << options.referenceFile << " " << fastqFilesTemp.i3 << " | awk '$1 !~ /@/' >> " << remappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFilesTemp.i3 << std::endl;
- return 1;
- }
-
- remove(toCString(fastqFilesTemp.i3));
-
- msg.str("");
- msg << "Converting BWA output " << remappedSam << " to bam format.";
- printStatus(msg);
-
- // Convert BWA output to bam.
- cmd.str("");
- cmd << SAMTOOLS << " view -S -h -b " << remappedSam << " > " << remappedUnsortedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while converting BWA output " << remappedSam << " to bam." << std::endl;
- return 1;
- }
- remove(toCString(remappedSam));
-
- msg.str("");
- msg << "Sorting " << remappedUnsortedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort bam file.
- cmd.str("");
- cmd << SAMTOOLS << " sort -@ " << options.threads << " -m " << options.memory << " -o " << remappedBam << " " << remappedUnsortedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting BWA output " << remappedUnsortedBam << std::endl;
- return 1;
- }
-
- msg.str("");
- msg << "Indexing " << remappedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Index bam file.
- cmd.str("");
- cmd << SAMTOOLS << " index " << remappedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while indexing BWA output " << remappedBam << std::endl;
- return 1;
- }
-
- msg.str("");
- msg << "Cropping unmapped reads from " << remappedBam;
- printStatus(msg);
-
- // Crop unmapped and create bam file of remapping.
- if (crop_unmapped(fastqFiles, remappedUnsortedBam, remappedBam, options.humanSeqs, NoAdapters(), options.alignment_score_factor) != 0)
- return 1;
- remove(toCString(remappedBai));
-
- msg.str("");
- msg << "Sorting " << remappedUnsortedBam << " by read name using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/remapped.bam by read name.
- cmd.str("");
- cmd << SAMTOOLS << " sort -n -@ " << options.threads << " -m " << options.memory << " -o " << remappedBam << " " << remappedUnsortedBam << " ";
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << remappedUnsortedBam << std::endl;
- return 1;
- }
-
- remove(toCString(remappedUnsortedBam));
-
- return 0;
-}
-
-
-
-#endif // #ifndef POPINS2_REMAPPING_H_
-
diff --git a/src/popins2.cpp b/src/popins4snake.cpp
similarity index 82%
rename from src/popins2.cpp
rename to src/popins4snake.cpp
index 7fa5eec85cc46d2c28b6ae9408a66c700d8858a2..79970ac70190c44339a388c9b1f02fdee3b44a4e 100644
--- a/src/popins2.cpp
+++ b/src/popins4snake.cpp
@@ -3,11 +3,8 @@
#include "argument_parsing.h" /* seqAn argument parser */
#include "popins2_crop_unmapped.h"
-#include "popins2_remapping.h"
#include "popins2_merge_and_set_mate.h"
#include "popins2_merge.h"
-#include "popins2_multik.h"
-#include "popins_contigmap.h"
#include "popins_find_locations.h"
#include "popins_place.h"
#include "popins_genotype.h"
@@ -34,11 +31,8 @@ int main(int argc, char const *argv[]){
const char * command = argv[1];
if (strcmp(command,"crop-unmapped") == 0) ret = popins2_crop_unmapped(argc, argv);
- else if (strcmp(command,"remapping") == 0) ret = popins2_remapping(argc, argv);
else if (strcmp(command,"merge-set-mate") == 0) ret = popins2_merge_and_set_mate(argc, argv);
else if (strcmp(command,"merge") == 0) ret = popins2_merge(argc, argv);
- else if (strcmp(command,"multik") == 0) ret = popins2_multik(argc, argv);
- else if (strcmp(command,"contigmap") == 0) ret = popins_contigmap(argc, argv);
else if (strcmp(command,"find-locations") == 0) ret = popins_find_locations(argc, argv);
else if (strcmp(command,"place-refalign") == 0) ret = popins_place_refalign(argc, argv);
else if (strcmp(command,"place-splitalign") == 0) ret = popins_place_splitalign(argc, argv);
diff --git a/external/gatb-minia-pipeline/BESST/BESST/__init__.py b/src/popins4snake.h
similarity index 100%
rename from external/gatb-minia-pipeline/BESST/BESST/__init__.py
rename to src/popins4snake.h
diff --git a/src/popins_contigmap.h b/src/popins_contigmap.h
deleted file mode 100644
index 3df8e7453fb8a4a94158065ef45f2369a5432712..0000000000000000000000000000000000000000
--- a/src/popins_contigmap.h
+++ /dev/null
@@ -1,306 +0,0 @@
-#ifndef POPINS_CONTIGMAP_H_
-#define POPINS_CONTIGMAP_H_
-
-#include <sstream>
-
-#include <seqan/file.h>
-#include <seqan/sequence.h>
-#include <seqan/bam_io.h>
-
-#include "util.h"
-#include "argument_parsing.h"
-#include "popins2_merge_and_set_mate.h"
-#include "location.h"
-
-using namespace seqan;
-
-// ==========================================================================
-// Function write_fastq()
-// ==========================================================================
-
-bool
-write_fastq(CharString & fastqFirst,
- CharString & fastqSecond,
- CharString & fastqSingle,
- CharString & unmappedBam)
-{
- typedef std::map<CharString, Pair<CharString> > TFastqMap;
-
- // Create maps for fastq records (first read in pair and second read in pair).
- TFastqMap firstReads, secondReads;
-
- // Open bam file.
- BamFileIn inStream(toCString(unmappedBam));
-
- // Read bam header and clear it since we don't need it.
- BamHeader header;
- readHeader(header, inStream);
- clear(header);
-
- // Open the output fastq files.
- SeqFileOut fastqFirstStream(toCString(fastqFirst));
- SeqFileOut fastqSecondStream(toCString(fastqSecond));
- SeqFileOut fastqSingleStream(toCString(fastqSingle));
-
- // Iterate over bam file and append fastq records.
- BamAlignmentRecord record;
- while(!atEnd(inStream))
- {
- readRecord(record, inStream);
- if (hasFlagUnmapped(record))
- appendFastqRecord(fastqFirstStream, fastqSecondStream, firstReads, secondReads, record);
- }
-
- // Write the fastq files.
- if (writeFastq(fastqFirstStream, fastqSecondStream, fastqSingleStream, firstReads, secondReads) != 0) return 1;
-
- return 0;
-}
-
-// ==========================================================================
-// Function fill_sequences()
-// ==========================================================================
-
-bool
-fill_sequences(CharString & outFile, CharString & inFile)
-{
- typedef Position<Dna5String>::Type TPos;
-
- BamFileIn inStream(toCString(inFile));
- BamFileOut outStream(context(inStream), toCString(outFile));
-
- BamHeader header;
- readHeader(header, inStream);
- writeHeader(outStream, header);
-
- BamAlignmentRecord firstRecord, nextRecord;
- while (!atEnd(inStream))
- {
- readRecord(nextRecord, inStream);
-
- if (firstRecord.qName != nextRecord.qName || hasFlagFirst(firstRecord) != hasFlagFirst(nextRecord))
- {
- // update first record
- firstRecord = nextRecord;
- if (length(firstRecord.seq) == 0 || length(firstRecord.qual) == 0)
- {
- std::cerr << "ERROR: First record of read " << firstRecord.qName << " has no sequence." << std::endl;
- return 1;
- }
- }
- else
- {
- // fill sequence field and quality string
- if (length(nextRecord.seq) == 0 || length(nextRecord.qual) == 0)
- {
- TPos last = length(nextRecord.cigar)-1;
- if (nextRecord.cigar[0].operation == 'H' || nextRecord.cigar[last].operation == 'H')
- {
- TPos begin = 0;
- if (nextRecord.cigar[0].operation == 'H')
- begin = nextRecord.cigar[0].count;
-
- TPos end = length(firstRecord.seq);
- if (nextRecord.cigar[last].operation == 'H')
- end -= nextRecord.cigar[last].count;
-
- nextRecord.seq = infix(firstRecord.seq, begin, end);
- nextRecord.qual = infix(firstRecord.qual, begin, end);
- }
- else
- {
- nextRecord.seq = firstRecord.seq;
- nextRecord.qual = firstRecord.qual;
- }
- }
- }
-
- writeRecord(outStream, nextRecord);
- }
-
- close(outStream);
-
- return 0;
-}
-
-
-// ==========================================================================
-// Function popins_contigmap()
-// ==========================================================================
-
-int popins_contigmap(int argc, char const ** argv)
-{
- // Parse the command line to get option values.
- ContigMapOptions options;
- ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
- if (res != ArgumentParser::PARSE_OK)
- return res;
-
- CharString workingDirectory = getFileName(options.prefix, options.sampleID);
-
- // Check for input files to exist.
- CharString fastqFirst = getFileName(workingDirectory, "paired.1.fastq");
- CharString fastqSecond = getFileName(workingDirectory, "paired.2.fastq");
- CharString fastqSingle = getFileName(workingDirectory, "single.fastq");
- CharString nonRefBam = getFileName(workingDirectory, "non_ref.bam");
- CharString nonRefNew = getFileName(workingDirectory, "non_ref_new.bam");
- CharString locationsFile = getFileName(workingDirectory, "locations.txt");
-
- if (!exists(fastqFirst) || !exists(fastqSecond) || !exists(fastqSingle) || !exists(nonRefBam))
- {
- std::cerr << "ERROR: Could not find all input files ";
- std::cerr << fastqFirst << ", " << fastqSecond << ", " << fastqSingle << ", and " << nonRefBam << std::endl;
- return 7;
- }
-
- unsigned nonContigSeqs = 0;
-
- std::ostringstream msg;
-
- if (!exists(nonRefNew))
- {
- // Create names of temporary files.
- CharString mappedSam = getFileName(workingDirectory, "contig_mapped_unsorted.sam");
- CharString mappedBamUnsorted = getFileName(workingDirectory, "contig_mapped_unsorted.bam");
- CharString mappedBam = getFileName(workingDirectory, "contig_mapped.bam");
- CharString mergedBam = getFileName(workingDirectory, "merged.bam");
-
- std::stringstream cmd;
-
- CharString indexFile = options.contigFile;
- indexFile += ".bwt";
- if (!exists(indexFile))
- {
- std::ostringstream msg;
- msg << "Indexing contigs in \'" << options.contigFile << "\' using " << BWA;
- printStatus(msg);
-
- cmd.str("");
- cmd << BWA << " index " << options.contigFile;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while indexing \'" << options.contigFile << "\' using " << BWA << std::endl;
- return 7;
- }
- }
-
- msg << "Mapping reads to contigs using " << BWA;
- printStatus(msg);
-
- // Remapping to contigs with bwa.
- cmd.str("");
- if (!options.bestAlignment) cmd << BWA << " mem -a ";
- else cmd << BWA << " mem ";
- cmd << "-t " << options.threads << " " << options.contigFile << " " << fastqFirst << " " << fastqSecond << " > " << mappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqFirst << " and " << fastqSecond << std::endl;
- return 7;
- }
- //remove(toCString(fastqFirst));
- //remove(toCString(fastqSecond));
-
- cmd.str("");
- if (!options.bestAlignment) cmd << BWA << " mem -a ";
- else cmd << BWA << " mem ";
- cmd << "-t " << options.threads << " " << options.contigFile << " " << fastqSingle << " | awk '$1 !~ /@/' >> " << mappedSam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while running bwa on " << fastqSingle << std::endl;
- return 7;
- }
- //remove(toCString(fastqSingle));
-
- printStatus("Filling in sequences of secondary records in bwa output");
-
- // Fill in sequences in bwa output.
- if (fill_sequences(mappedBamUnsorted, mappedSam) != 0)
- {
- return 7;
- }
- remove(toCString(mappedSam));
-
- msg.str("");
- msg << "Sorting " << mappedBamUnsorted << " by read name using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/contig_mapped.bam by read name
- cmd.str("");
- cmd << SAMTOOLS << " sort -n -@ " << options.threads << " -m " << options.memory << " -o " << mappedBam << " " << mappedBamUnsorted;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << mappedBamUnsorted << " by read name using " << SAMTOOLS << std::endl;
- return 7;
- }
- remove(toCString(mappedBamUnsorted));
-
- // Merge non_ref.bam with contig_mapped and set the mates.
- if (merge_and_set_mate(mergedBam, nonContigSeqs, nonRefBam, mappedBam) != 0)
- return 7;
-
- remove(toCString(mappedBam));
- //remove(toCString(nonRefBam));
-
- msg.str("");
- msg << "Sorting " << mergedBam << " using " << SAMTOOLS;
- printStatus(msg);
-
- // Sort <WD>/merged.bam by beginPos, output is <WD>/non_ref.bam.
- cmd.str("");
- cmd << SAMTOOLS << " sort -@ " << options.threads << " -m " << options.memory << " -o " << nonRefNew << " " << mergedBam;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while sorting " << mergedBam << " by beginPos using " << SAMTOOLS << std::endl;
- return 7;
- }
- remove(toCString(mergedBam));
-
- msg.str("");
- msg << "Indexing " << nonRefNew << " by beginPos using " << SAMTOOLS;
- printStatus(msg);
-
- // Index <WD>/non_ref_new.bam.
- cmd.str("");
- cmd << SAMTOOLS << " index " << nonRefNew;
- if (system(cmd.str().c_str()) != 0)
- {
- std::cerr << "ERROR while indexing " << nonRefNew << " using " << SAMTOOLS << std::endl;
- return 7;
- }
- }
- else
- {
- BamFileIn nonRefStream(toCString(nonRefBam));
- BamHeader header;
- readHeader(header, nonRefStream);
- nonContigSeqs = length(contigNames(context(nonRefStream)));
- }
-
- msg.str("");
- msg << "Reading chromosomes from " << options.referenceFile;
- printStatus(msg);
-
- std::set<CharString> chromosomes;
- if (readChromosomes(chromosomes, options.referenceFile) != 0)
- return 7;
-
- msg.str("");
- msg << "Computing contig locations from anchoring reads in " << nonRefNew;
- printStatus(msg);
-
- // Find anchoring locations of contigs for this individual.
- String<Location> locations;
- findLocations(locations, nonRefNew, chromosomes, nonContigSeqs, options.maxInsertSize);
- scoreLocations(locations);
- if (writeLocations(locationsFile, locations) != 0) return 7;
-
- // Remove the non_ref_new.bam file.
- if (options.deleteNonRefNew)
- remove(toCString(nonRefNew));
-
- return 0;
-}
-
-#endif // #ifndef POPINS_CONTIGMAP_H_
-
-
diff --git a/src/popins_genotype.h b/src/popins_genotype.h
index e75d3a1883913613d4e29bcbd52431c74ab3b444..69a4b394a89ae7269772e1de874fc26141dfc6be 100644
--- a/src/popins_genotype.h
+++ b/src/popins_genotype.h
@@ -123,7 +123,7 @@ popins_genotype(int argc, char const ** argv)
// Open the bam file. (A bam file needs the bai index and the bam file stream.)
BamIndex<Bai> bamIndex;
BamFileIn bamStream;
- if (initializeBam(toCString(sampleInfo.bam_file), bamIndex, bamStream) != 0)
+ if (initializeBam(sampleInfo.bam_file, bamIndex, bamStream) != 0)
return 7;
// Build an index of the insertion sequences' fasta file.
@@ -141,7 +141,7 @@ popins_genotype(int argc, char const ** argv)
BamIndex<Bai> bamIndexAlt;
BamFileIn bamStreamAlt;
CharString altBamFile = getFileName(samplePath, "non_ref_new.bam");
- if (initializeBam(toCString(altBamFile), bamIndexAlt, bamStreamAlt))
+ if (initializeBam(altBamFile, bamIndexAlt, bamStreamAlt))
return 7;
std::ostringstream msg;
diff --git a/src/variant_caller.h b/src/variant_caller.h
index 5d7a33e84b4d695ff02280dc6740a89484c88564..31e84fadf0699770f37b39cba0c0fea95a0e6f00 100644
--- a/src/variant_caller.h
+++ b/src/variant_caller.h
@@ -654,18 +654,17 @@ int variantCallRegion(VcfRecord & variant, VcfFileIn & vcfS,
}
-int initializeBam(char* fileName, BamIndex<Bai> & bamIndex, BamFileIn & bamStream)
+int initializeBam(CharString fileName, BamIndex<Bai> & bamIndex, BamFileIn & bamStream)
{
- if (!open(bamStream, fileName))
+ if (!open(bamStream, toCString(fileName)))
{
std::cerr << "ERROR: Could not open " << fileName << " for reading.\n";
return 1;
}
- char baifileName[strlen(fileName) + 10];
- strcpy(baifileName, fileName);
- strcat(baifileName, ".bai");
- if (!open(bamIndex, baifileName))
+ CharString baifileName = fileName;
+ fileName += ".bai";
+ if (!open(bamIndex, toCString(baifileName)))
{
std::cerr << "ERROR: Could not read BAI index file " << fileName << "\n";
return 1;