Commit 1c419d6e authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing pipe command

(cherry picked from commit e4baa723)
parent 3019cf79
......@@ -34,17 +34,19 @@ class SamtoolsView(val root: Configurable) extends Samtools {
var F: List[String] = config("F", default = List.empty[String])
def cmdBase = required(executable) +
@Input(required = false)
var L: Option[File] = None
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 {
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment