crop-unmapped with even more flexibility of the input parameters, se, pe1, pe2

The FASTQ input file names can now be specified as parameters se, pe1, pe2

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);