From 2fa1d42264e20cc4188fb6958ac6d576f8d3b24b Mon Sep 17 00:00:00 2001
From: Birte Kehr <birte.kehr@bihealth.de>
Date: Thu, 25 Aug 2022 19:37:23 +0200
Subject: [PATCH] Adding back an option to suppress printing the
POPINS_SAMPLE_INFO file.
---
src/argument_parsing.h | 9 ++++++-
src/popins2_crop_unmapped.h | 54 +++++++++++++++++--------------------
2 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/src/argument_parsing.h b/src/argument_parsing.h
index 2579147..0114cf4 100644
--- a/src/argument_parsing.h
+++ b/src/argument_parsing.h
@@ -38,6 +38,8 @@ struct CropUnmappedOptions {
float alignment_score_factor;
+ bool printSampleInfo;
+
CropUnmappedOptions () :
matesBam("mates.bam"),
pe1("paired.1.fastq"),
@@ -46,7 +48,8 @@ struct CropUnmappedOptions {
prefix("."),
sampleID(""),
humanSeqs(maxValue<int>()),
- alignment_score_factor(0.67f)
+ alignment_score_factor(0.67f),
+ printSampleInfo(true)
{}
};
@@ -251,6 +254,8 @@ bool getOptionValues(CropUnmappedOptions & options, ArgumentParser const & parse
getOptionValue(options.humanSeqs, parser, "filter");
if (isSet(parser, "alignment-score-factor"))
getOptionValue(options.alignment_score_factor, parser, "alignment-score-factor");
+ if (isSet(parser, "noSampleInfo"))
+ options.printSampleInfo = false;
return true;
}
@@ -569,6 +574,7 @@ void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
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("m", "mates", "File name for the aligned mates BAM file.", ArgParseArgument::OUTPUT_FILE, "BAM FILE"));
+ addOption(parser, ArgParseOption("i", "noSampleInfo", "Do not print sample information to POPINS_SAMPLE_INFO file in sample directory."));
addSection(parser, "Algorithm options");
addOption(parser, ArgParseOption("a", "adapters", "Enable adapter removal for Illumina reads. Default: \\fIno adapter removal\\fP.", ArgParseArgument::STRING, "STR"));
@@ -589,6 +595,7 @@ void setupParser(ArgumentParser & parser, CropUnmappedOptions & options){
setDefaultValue(parser, "prefix", "\'.\'");
setDefaultValue(parser, "sample", "retrieval from BAM file header");
setDefaultValue(parser, "alignment-score-factor", options.alignment_score_factor);
+ setDefaultValue(parser, "noSampleInfo", "false");
setMinValue(parser, "alignment-score-factor", "0.0");
setMaxValue(parser, "alignment-score-factor", "1.0");
diff --git a/src/popins2_crop_unmapped.h b/src/popins2_crop_unmapped.h
index 4d64020..ea24a52 100644
--- a/src/popins2_crop_unmapped.h
+++ b/src/popins2_crop_unmapped.h
@@ -79,44 +79,38 @@ int popins2_crop_unmapped(int argc, char const ** argv){
CharString fastqSingle = getFileName(workingDirectory, options.se);
Triple<CharString> fastqFiles = Triple<CharString>(fastqFirst, fastqSecond, fastqSingle);
+ 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;
+ }
- // check if files already exits
- std::fstream stream(toCString(fastqFirst));
- if (!stream.is_open())
+ if (options.printSampleInfo)
{
+ CharString sampleInfoFile = getFileName(workingDirectory, "POPINS_SAMPLE_INFO");
+ writeSampleInfo(info, sampleInfoFile);
+
msg.str("");
- msg << "Cropping unmapped reads from " << options.mappingFile;
+ msg << "Sample info written to \'" << sampleInfoFile << "\'.";
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);
-
}
return res;
-
}
#endif // #ifndef POPINS2_CROP_UNMAPPED_H_
--
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