Commit d2c7fc48 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed bam input

parent 7d179c4e
......@@ -105,8 +105,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
override def keepFinalBamfile: Boolean = super.keepFinalBamfile && !useIndelRealigner && !useBaseRecalibration
override def bamFile: Option[Mapping#File] = mapping.map(_.mergedBamFile)
override def preProcessBam: Option[Mapping#File] = if (useIndelRealigner && usePrintReads && useBaseRecalibration)
bamFile.map(swapExt(libDir, _, ".bam", ".realign.baserecal.bam"))
else if (useIndelRealigner) bamFile.map(swapExt(libDir, _, ".bam", ".realign.bam"))
......
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