From 8912e43c46f4bdccd316f3b72ac2799557311596 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <krannich479@googlemail.com>
Date: Thu, 10 Mar 2022 12:22:17 +0100
Subject: [PATCH] crop-unmapped with even more flexibility of the input
parameters, se, pe1, pe2
---
Makefile | 2 +-
src/argument_parsing.h | 22 ++++++++++++++++++++++
src/popins2_crop_unmapped.h | 9 ++++++---
3 files changed, 29 insertions(+), 4 deletions(-)
diff --git a/Makefile b/Makefile
index 218f6c5..b5e8591 100644
--- a/Makefile
+++ b/Makefile
@@ -18,7 +18,7 @@ TOOLS=-DSAMTOOLS=\"$(SAMTOOLS)\" -DBWA=\"$(BWA)\" -DSICKLE=\"$(SICKLE)\" -DVELVE
# Date and version number from git
DATE := on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1)
-VERSION := 0.0.3-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
+VERSION := 0.0.4-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
CXXFLAGS += -DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\"
# Compiler flags
diff --git a/src/argument_parsing.h b/src/argument_parsing.h
index 87a38d7..e03cf5d 100644
--- a/src/argument_parsing.h
+++ b/src/argument_parsing.h
@@ -58,6 +58,9 @@ struct AssemblyOptions {
struct CropUnmappedOptions {
CharString outputFile;
+ CharString pe1;
+ CharString pe2;
+ CharString se;
CharString mappingFile;
CharString matepairFile;
@@ -79,6 +82,9 @@ struct CropUnmappedOptions {
CropUnmappedOptions () :
outputFile("mates.bam"),
+ pe1("paired.1.fastq"),
+ pe2("paired.2.fastq"),
+ se("single.fastq"),
matepairFile(""),
referenceFile(""),
prefix("."),
@@ -366,6 +372,13 @@ bool getOptionValues(CropUnmappedOptions & options, ArgumentParser const & parse
if (isSet(parser, "output"))
getOptionValue(options.outputFile, parser, "output");
+ if (isSet(parser, "paired1"))
+ getOptionValue(options.pe1, parser, "paired1");
+ if (isSet(parser, "paired2"))
+ getOptionValue(options.pe2, parser, "paired2");
+ if (isSet(parser, "single"))
+ getOptionValue(options.se, parser, "single");
+
if (isSet(parser, "prefix"))
getOptionValue(options.prefix, parser, "prefix");
if (isSet(parser, "sample"))
@@ -828,6 +841,9 @@ void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
// Setup the options.
addSection(parser, "Input/output options");
addOption(parser, ArgParseOption("o", "output", "File name for the output BAM file.", ArgParseArgument::OUTPUT_FILE, "BAM FILE"));
+ addOption(parser, ArgParseOption("pe1", "paired1", "File name for the first reads file.", ArgParseArgument::INPUT_FILE, "FASTQ FILE"));
+ addOption(parser, ArgParseOption("pe2", "paired2", "File name for the second reads file.", ArgParseArgument::INPUT_FILE, "FASTQ FILE"));
+ addOption(parser, ArgParseOption("se", "single", "File name for the single reads file.", ArgParseArgument::INPUT_FILE, "FASTQ FILE"));
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"));
@@ -848,6 +864,12 @@ void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
setValidValues(parser, "adapters", "HiSeq HiSeqX");
setValidValues(parser, "reference", "fa fna fasta gz");
setDefaultValue(parser, "output", options.outputFile);
+ setDefaultValue(parser, "paired1", options.pe1);
+ setValidValues(parser, "paired1", "fq fastq gz");
+ setDefaultValue(parser, "paired2", options.pe2);
+ setValidValues(parser, "paired2", "fq fastq gz");
+ setDefaultValue(parser, "single", options.se);
+ setValidValues(parser, "single", "fq fastq gz");
setDefaultValue(parser, "prefix", "\'.\'");
setDefaultValue(parser, "sample", "retrieval from BAM file header");
setDefaultValue(parser, "kmerLength", options.kmerLength);
diff --git a/src/popins2_crop_unmapped.h b/src/popins2_crop_unmapped.h
index 7c7a940..c972551 100644
--- a/src/popins2_crop_unmapped.h
+++ b/src/popins2_crop_unmapped.h
@@ -75,9 +75,12 @@ int popins2_crop_unmapped(int argc, char const ** argv){
//CharString matesBam = getFileName(workingDirectory, "mates.bam");
CharString matesBam = getFileName(workingDirectory, options.outputFile);
- CharString fastqFirst = getFileName(workingDirectory, "paired.1.fastq");
- CharString fastqSecond = getFileName(workingDirectory, "paired.2.fastq");
- CharString fastqSingle = getFileName(workingDirectory, "single.fastq");
+ //CharString fastqFirst = getFileName(workingDirectory, "paired.1.fastq");
+ //CharString fastqSecond = getFileName(workingDirectory, "paired.2.fastq");
+ //CharString fastqSingle = getFileName(workingDirectory, "single.fastq");
+ CharString fastqFirst = getFileName(workingDirectory, options.pe1);
+ CharString fastqSecond = getFileName(workingDirectory, options.pe2);
+ CharString fastqSingle = getFileName(workingDirectory, options.se);
Triple<CharString> fastqFiles = Triple<CharString>(fastqFirst, fastqSecond, fastqSingle);
--
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