Commit 712422bb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-272' into 'develop'

Make inverse of the boolean to fix issue #272

Fixes #272 

See merge request !319
parents eb605a1f 0372b00e
......@@ -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?")
}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment