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

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;
 }
 
 

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");