Commit e4baa723 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing pipe command

parent 62878275
...@@ -36,19 +36,16 @@ class SamtoolsView(val root: Configurable) extends Samtools { ...@@ -36,19 +36,16 @@ class SamtoolsView(val root: Configurable) extends Samtools {
@Input(required = false) @Input(required = false)
var L: Option[File] = None var L: Option[File] = None
def cmdBase = required(executable) + def cmdLine = required(executable) +
required("view") + required("view") +
optional("-q", q) + optional("-q", q) +
optional("-L", L) + optional("-L", L) +
repeat("-f", f) + repeat("-f", f) +
repeat("-F", F) + repeat("-F", F) +
conditional(b, "-b") + conditional(b, "-b") +
conditional(h, "-h") conditional(h, "-h") +
def cmdPipeInput = cmdBase + "-" (if (inputAsStdin) "-" else required(input)) +
def cmdPipe = cmdBase + required(input) (if (outputAsStsout) "" else " > " + required(output))
/** Returns command to execute */
def cmdLine = cmdPipe + " > " + required(output)
} }
object SamtoolsView { object SamtoolsView {
......
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