Commit 2da7887f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove old code

parent 650352d4
......@@ -336,18 +336,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
bwaCommand.isIntermediate = true
val sortSam = new SortSam(this)
sortSam.output = output
if (config("use_pipes", default = true).asBoolean) {
//val samtoolsSort = new SamtoolsSort(this)
//samtoolsSort.outputFormat = Some("bam")
//samtoolsSort.output = output
add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
} else {
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
add(bwaCommand)
sortSam.input = bwaCommand.output
sortSam.isIntermediate = chunking || !skipMarkduplicates
add(sortSam)
}
add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
output
}
......
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