Commit 483ba923 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding option to extension

parent e5ccc0cf
......@@ -44,6 +44,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
var minAP: Option[Int] = config("min_ap")
var homoFraction: Option[Double] = config("homoFraction")
var ploidy: Option[Int] = config("ploidy")
var refCalls: Boolean = config("ref_calls", default = false)
var sample: String = _
var reference: String = _
......@@ -72,6 +73,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
optional("--minAP", minAP) +
optional("--homoFraction", homoFraction) +
optional("--ploidy", ploidy) +
conditional(refCalls, "--refCalls") +
required("--sample", sample) +
(if (inputAsStdin) "" else required("-I", inputMpileup))
}
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