Commit cae64a35 authored by Moustakas's avatar Moustakas
Browse files

Add text to options parser

parent 7e3e31cb
......@@ -47,19 +47,19 @@ object CheckAllelesVcfInBam extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
}
} text "VCF file"
opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputFile = x)
}
} text "output VCF file name"
opt[String]('s', "sample") unbounded () minOccurs 1 action { (x, c) =>
c.copy(samples = x :: c.samples)
}
} text "sample name"
opt[File]('b', "bam") unbounded () minOccurs 1 action { (x, c) =>
c.copy(bamFiles = x :: c.bamFiles)
}
} text "bam file, from which the variants (VCF files) were called"
opt[Int]('m', "min_mapping_quality") maxOccurs 1 action { (x, c) =>
c.copy(minMapQual = c.minMapQual)
}
} text "minimum mapping quality score for a read to be taken into account"
}
private class CountReport(
......
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