Commit 4d722319 authored by rhpvorderman's avatar rhpvorderman

Merge remote-tracking branch 'origin' into Fix-BIOPET-479

parents 1825f7be 42e2ffe3
......@@ -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"))
......@@ -189,7 +187,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
Some(makeVariantcalling(multisample = false, sample = Some(sampleId)))
} else None
override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner || (libraries.size == 1))
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
......
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