Commit b75b9047 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed pipe command of samtools flagstats

parent e4baa723
......@@ -28,7 +28,9 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
var output: File = _
/** Returns command to execute */
def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
def cmdLine = required(executable) + required("flagstat") +
(if (inputAsStdin) "-" else required(input)) +
(if (outputAsStsout) "" else " > " + required(output))
}
object SamtoolsFlagstat {
......
......@@ -79,6 +79,8 @@ class BiosBaseCounts(val root: Configurable) extends QScript with Measurement wi
val samtoolsView = new SamtoolsView(this)
samtoolsView.input = bamFile
samtoolsView.b = true
samtoolsView.h = true
samtoolsView.L = Some(annotationBed)
val samtoolsFlagstat = new SamtoolsFlagstat(this)
samtoolsFlagstat.output = new File(outputDir, s"$sampleName.exon.flagstat")
......
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