Commit 8e73d322 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed pipe command of samtools flagstats

(cherry picked from commit b75b9047)
parent 1c419d6e
......@@ -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 {
......
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