Commit 9d0abb92 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix mpileup

parent 818741d1
......@@ -72,6 +72,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
override def commandLine = {
(if (inputMpileup == null) {
val samtoolsMpileup = new SamtoolsMpileup(this)
samtoolsMpileup.reference = referenceFasta()
samtoolsMpileup.input = List(inputBam)
samtoolsMpileup.cmdPipe + " | "
} else "") +
......
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