Commit 039c58a9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added text to cmdArgs

parent 378dc2a3
......@@ -29,19 +29,19 @@ object BamStats extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('R', "reference") valueName "<file>" action { (x, c) =>
c.copy(referenceFasta = Some(x))
}
} text "Fasta file of reference"
opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
c.copy(outputDir = x)
}
} text "Output directory"
opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
c.copy(bamFile = x)
}
} text "Input bam file"
opt[Int]("binSize") valueName "<int>" action { (x, c) =>
c.copy(binSize = x)
}
} text "Bin size of stats (beta)"
opt[Int]("threadBinSize") valueName "<int>" action { (x, c) =>
c.copy(threadBinSize = x)
}
} text "Size of region per thread"
}
/** This is the main entry to [[BamStats]], this will do the argument parsing. */
......
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