From 46c6651d56051a52deef372bd4a5fe7aa1bf6414 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <krannich479@googlemail.com>
Date: Thu, 20 Jan 2022 15:39:35 +0100
Subject: [PATCH] new I/O for the crop-unmapped module
---
Makefile | 2 +-
src/argument_parsing.h | 19 +++++++++++++++++--
src/popins2_crop_unmapped.h | 20 +++++++++++---------
src/popins_find_locations.h | 2 ++
4 files changed, 31 insertions(+), 12 deletions(-)
diff --git a/Makefile b/Makefile
index 45eb510..218f6c5 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 $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1)
-VERSION := 0.0.2-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
+VERSION := 0.0.3-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 1d7c375..87a38d7 100644
--- a/src/argument_parsing.h
+++ b/src/argument_parsing.h
@@ -56,6 +56,9 @@ struct AssemblyOptions {
struct CropUnmappedOptions {
+
+ CharString outputFile;
+
CharString mappingFile;
CharString matepairFile;
CharString referenceFile;
@@ -72,7 +75,10 @@ struct CropUnmappedOptions {
float alignment_score_factor;
+ bool printSampleInfo;
+
CropUnmappedOptions () :
+ outputFile("mates.bam"),
matepairFile(""),
referenceFile(""),
prefix("."),
@@ -81,7 +87,8 @@ struct CropUnmappedOptions {
humanSeqs(maxValue<int>()),
threads(1),
memory("768M"),
- alignment_score_factor(0.67f)
+ alignment_score_factor(0.67f),
+ printSampleInfo(false)
{}
};
@@ -357,6 +364,8 @@ bool getOptionValues(CropUnmappedOptions & options, ArgumentParser const & parse
getArgumentValue(options.mappingFile, parser, 0);
+ if (isSet(parser, "output"))
+ getOptionValue(options.outputFile, parser, "output");
if (isSet(parser, "prefix"))
getOptionValue(options.prefix, parser, "prefix");
if (isSet(parser, "sample"))
@@ -377,6 +386,8 @@ bool getOptionValues(CropUnmappedOptions & options, ArgumentParser const & parse
getOptionValue(options.memory, parser, "memory");
if (isSet(parser, "alignment-score-factor"))
getOptionValue(options.alignment_score_factor, parser, "alignment-score-factor");
+ if (isSet(parser, "printSampleInfo"))
+ options.printSampleInfo = true;
return true;
}
@@ -816,9 +827,11 @@ 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("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"));
+ addOption(parser, ArgParseOption("i", "printSampleInfo", "Prints sample information sheet if set."));
addSection(parser, "Algorithm options");
addOption(parser, ArgParseOption("a", "adapters", "Enable adapter removal for Illumina reads. Default: \\fIno adapter removal\\fP.", ArgParseArgument::STRING, "STR"));
@@ -834,12 +847,14 @@ void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
// Set valid and default values.
setValidValues(parser, "adapters", "HiSeq HiSeqX");
setValidValues(parser, "reference", "fa fna fasta gz");
+ setDefaultValue(parser, "output", options.outputFile);
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);
+ setDefaultValue(parser, "printSampleInfo", "false");
setMinValue(parser, "threads", "1");
setMinValue(parser, "alignment-score-factor", "0.0");
@@ -1720,7 +1735,7 @@ void printMultikOptions(const MultikOptions &options){
}
-void printMultikOptions(const FindLocationsOptions &options){
+void printFindLocationsOptions(const FindLocationsOptions &options){
cout << "=========================================================" << endl;
cout << "popins version : " << VERSION << endl;
cout << "PARAMETER ======== : VALUE ==============================" << endl;
diff --git a/src/popins2_crop_unmapped.h b/src/popins2_crop_unmapped.h
index 5da97c4..7c7a940 100644
--- a/src/popins2_crop_unmapped.h
+++ b/src/popins2_crop_unmapped.h
@@ -46,8 +46,8 @@ bool retrieveSampleID(CharString & sampleID, CharString & mappingBam)
// Function popins2_crop_unmapped()
// ==========================================================================
-int popins2_crop_unmapped(int argc, char const ** argv)
-{
+int popins2_crop_unmapped(int argc, char const ** argv){
+
std::ostringstream msg;
// Parse the command line to get option values.
@@ -73,7 +73,8 @@ int popins2_crop_unmapped(int argc, char const ** argv)
float as_factor = options.alignment_score_factor;
- CharString matesBam = getFileName(workingDirectory, "mates.bam");
+ //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");
@@ -106,13 +107,14 @@ int popins2_crop_unmapped(int argc, char const ** argv)
return 7;
}
- CharString sampleInfoFile = getFileName(workingDirectory, "POPINS_SAMPLE_INFO");
- writeSampleInfo(info, sampleInfoFile);
-
- msg.str("");
- msg << "Sample info written to \'" << sampleInfoFile << "\'.";
- printStatus(msg);
+ if(options.printSampleInfo){
+ CharString sampleInfoFile = getFileName(workingDirectory, "POPINS_SAMPLE_INFO");
+ writeSampleInfo(info, sampleInfoFile);
+ msg.str("");
+ msg << "Sample info written to \'" << sampleInfoFile << "\'.";
+ printStatus(msg);
+ }
}
diff --git a/src/popins_find_locations.h b/src/popins_find_locations.h
index 82e1778..abce682 100644
--- a/src/popins_find_locations.h
+++ b/src/popins_find_locations.h
@@ -133,6 +133,8 @@ int popins_find_locations(int argc, char const ** argv){
if (res != ArgumentParser::PARSE_OK)
return res;
+ printFindLocationsOptions(options);
+
CharString workingDirectory = getFileName(options.prefix, options.sampleID);
// Check for input files to exist.
--
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