Commit 0372b00e authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Make inverse of the boolean to fix issue #272

parent acbbc173
......@@ -183,13 +183,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
case (MergeStrategy.PreProcessMergeSam | MergeStrategy.PreProcessMarkDuplicates) if libraries.flatMap(_._2.preProcessBam).size == 1 =>
add(Ln.linkBamFile(qscript, libraries.flatMap(_._2.preProcessBam).head, bamFile.get): _*)
case MergeStrategy.MergeSam =>
add(MergeSamFiles(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = keepMergedFiles))
add(MergeSamFiles(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = !keepMergedFiles))
case MergeStrategy.PreProcessMergeSam =>
add(MergeSamFiles(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = keepMergedFiles))
add(MergeSamFiles(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = !keepMergedFiles))
case MergeStrategy.MarkDuplicates =>
add(MarkDuplicates(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = keepMergedFiles))
add(MarkDuplicates(qscript, libraries.flatMap(_._2.bamFile).toList, bamFile.get, isIntermediate = !keepMergedFiles))
case MergeStrategy.PreProcessMarkDuplicates =>
add(MarkDuplicates(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = keepMergedFiles))
add(MarkDuplicates(qscript, libraries.flatMap(_._2.preProcessBam).toList, bamFile.get, isIntermediate = !keepMergedFiles))
case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
}
......
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