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