From 21a8baad99a82c8098c0a77be11e3a930e6d33f2 Mon Sep 17 00:00:00 2001
From: Thomas Krannich <krannich479@googlemail.com>
Date: Wed, 16 Mar 2022 12:24:35 +0100
Subject: [PATCH] add IO of non-ref alignment file name
---
Makefile | 2 +-
src/argument_parsing.h | 30 +++++++++++++++++++++---------
src/popins_find_locations.h | 2 +-
3 files changed, 23 insertions(+), 11 deletions(-)
diff --git a/Makefile b/Makefile
index b5e8591..9340625 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 $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1)
-VERSION := 0.0.4-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
+VERSION := 0.0.6-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 e03cf5d..879ec93 100644
--- a/src/argument_parsing.h
+++ b/src/argument_parsing.h
@@ -243,6 +243,7 @@ struct FindLocationsOptions {
CharString prefix;
CharString sampleID;
CharString referenceFile;
+ CharString non_ref_bam;
int maxInsertSize;
bool deleteNonRefNew;
@@ -251,6 +252,7 @@ struct FindLocationsOptions {
prefix("."),
sampleID(""),
referenceFile("genome.fa"),
+ non_ref_bam("non_ref.bam"),
maxInsertSize(800),
deleteNonRefNew(false)
{}
@@ -568,6 +570,8 @@ bool getOptionValues(FindLocationsOptions &options, seqan::ArgumentParser &parse
getOptionValue(options.prefix, parser, "prefix");
if (isSet(parser, "reference"))
getOptionValue(options.referenceFile, parser, "reference");
+ if (isSet(parser, "non-ref"))
+ getOptionValue(options.non_ref_bam, parser, "non-ref");
if (isSet(parser, "maxInsertSize"))
getOptionValue(options.maxInsertSize, parser, "maxInsertSize");
if (isSet(parser, "delNonRefNew"))
@@ -1123,6 +1127,7 @@ void setupParser(seqan::ArgumentParser &parser, FindLocationsOptions &options){
addSection(parser, "Input/output options");
addOption(parser, ArgParseOption("p", "prefix", "Path to the sample directories.", ArgParseArgument::STRING, "PATH"));
addOption(parser, ArgParseOption("r", "reference", "Name of reference genome file.", ArgParseArgument::INPUT_FILE, "FASTA_FILE"));
+ addOption(parser, ArgParseOption("n", "non-ref", "Non-reference reads alignment file name.", ArgParseArgument::INPUT_FILE, "BAM FILE"));
addSection(parser, "Algorithm options");
addOption(parser, ArgParseOption("e", "maxInsertSize", "The maximum expected insert size of the read pairs.", ArgParseArgument::INTEGER, "INT"));
@@ -1134,6 +1139,7 @@ void setupParser(seqan::ArgumentParser &parser, FindLocationsOptions &options){
// Set default values.
setDefaultValue(parser, "prefix", "\'.\'");
setDefaultValue(parser, "reference", options.referenceFile);
+ setDefaultValue(parser, "non-ref", options.non_ref_bam);
setDefaultValue(parser, "maxInsertSize", options.maxInsertSize);
setDefaultValue(parser, "delNonRefNew", "false");
@@ -1578,6 +1584,11 @@ ArgumentParser::ParseResult checkInput(FindLocationsOptions &options){
res = ArgumentParser::PARSE_ERROR;
}
+ if (!exists(options.non_ref_bam)){
+ std::cerr << "ERROR: Non-reference reads input file \'" << options.non_ref_bam << "\' does not exist." << std::endl;
+ res = ArgumentParser::PARSE_ERROR;
+ }
+
return res;
}
@@ -1758,15 +1769,16 @@ void printMultikOptions(const MultikOptions &options){
void printFindLocationsOptions(const FindLocationsOptions &options){
- cout << "=========================================================" << endl;
- cout << "popins version : " << VERSION << endl;
- cout << "PARAMETER ======== : VALUE ==============================" << endl;
- cout << "prefix : " << options.prefix << endl;
- cout << "sample ID : " << options.sampleID << endl;
- cout << "reference file : " << options.referenceFile << endl;
- cout << "max insert size : " << options.maxInsertSize << endl;
- cout << "delete non_ref_new : " << options.deleteNonRefNew << endl;
- cout << "=========================================================" << endl;
+ cout << "==========================================================" << endl;
+ cout << "popins version : " << VERSION << endl;
+ cout << "PARAMETER ========= : VALUE ==============================" << endl;
+ cout << "prefix : " << options.prefix << endl;
+ cout << "sample ID : " << options.sampleID << endl;
+ cout << "reference file : " << options.referenceFile << endl;
+ cout << "non-reference reads : " << options.non_ref_bam << endl;
+ cout << "max insert size : " << options.maxInsertSize << endl;
+ cout << "delete non_ref_new : " << options.deleteNonRefNew << endl;
+ cout << "==========================================================" << endl;
}
diff --git a/src/popins_find_locations.h b/src/popins_find_locations.h
index abce682..dc98eae 100644
--- a/src/popins_find_locations.h
+++ b/src/popins_find_locations.h
@@ -141,7 +141,7 @@ int popins_find_locations(int argc, char const ** argv){
//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 nonRefBam = getFileName(workingDirectory, options.non_ref_bam);
CharString nonRefNew = getFileName(workingDirectory, "non_ref_new.bam");
CharString locationsFile = getFileName(workingDirectory, "locations.txt");
--
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