Commit d011c785 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into fix-BIOPET-583

parents 5ea017ca 3c83710e
......@@ -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 {
......
......@@ -33,18 +33,20 @@ class SamtoolsView(val root: Configurable) extends Samtools {
var f: List[String] = config("f", default = List.empty[String])
var F: List[String] = config("F", default = List.empty[String])
def cmdBase = required(executable) +
@Input(required = false)
var L: Option[File] = None
/** Returns command to execute */
def cmdLine = required(executable) +
required("view") +
optional("-q", q) +
optional("-L", L) +
repeat("-f", f) +
repeat("-F", F) +
conditional(b, "-b") +
conditional(h, "-h")
def cmdPipeInput = cmdBase + "-"
def cmdPipe = cmdBase + required(input)
/** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
conditional(h, "-h") +
(if (inputAsStdin) "-" else required(input)) +
(if (outputAsStsout) "" else " > " + required(output))
}
object SamtoolsView {
......
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