Commit 1b9ceb90 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix bug on mpileup

parent e995516a
......@@ -146,8 +146,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
add(vcfFilter)
scriptOutput.rawFilterVcfFile = vcfFilter.outputVcf
} else if (rawVcfInput != null) scriptOutput.rawFilterVcfFile = rawVcfInput
if (scriptOutput.rawFilterVcfFile == null) throw new IllegalStateException("Files can't be empty")
mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
if (scriptOutput.rawFilterVcfFile != null) mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
}
// Allele mode
......
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