Commit 6a83d167 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add output arg to biopet flagstat

parent f2d40822
......@@ -61,12 +61,18 @@ object BiopetFlagstat extends ToolCommand {
flagstat
}
case class Args(inputFile: File = null, summaryFile: Option[File] = None, region: Option[String] = None) extends AbstractArgs
case class Args(inputFile: File = null,
outputFile: Option[File] = None,
summaryFile: Option[File] = None,
region: Option[String] = None) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
} text "input bam file"
opt[File]('o', "outputFile") valueName "<file>" action { (x, c) =>
c.copy(outputFile = Some(x))
} text "output file"
opt[File]('s', "summaryFile") valueName "<file>" action { (x, c) =>
c.copy(summaryFile = Some(x))
} text "summary output file"
......@@ -151,7 +157,14 @@ object BiopetFlagstat extends ToolCommand {
writer.close()
}
println(flagstatCollector.report)
commandArgs.outputFile match {
case Some(file) => {
val writer = new PrintWriter(file)
writer.println(flagstatCollector.report)
writer.close()
}
case _ => println(flagstatCollector.report)
}
}
class FlagstatCollector {
......
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