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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-09-01 18:14:45 -04:00
parent d2a33beff7 e253f6f05d
commit ad4ea0b80b
1 changed files with 1 additions and 1 deletions
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2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -159,7 +159,7 @@ class DataProcessingPipeline extends QScript {
for (rg <- readGroups) {
val intermediateInBam: File = if (index == readGroups.length) { inBam } else { swapExt(outBam, ".bam", index+1 + "-rg.bam") }
val intermediateOutBam: File = if (index > 1) {swapExt(outBam, ".bam", index + "-rg.bam") } else { outBam}
val readGroup = new ReadGroup(rg.getReadGroupId, rg.getPlatform, rg.getLibrary, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription)
val readGroup = new ReadGroup(rg.getReadGroupId, rg.getLibrary, rg.getPlatform, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription)
add(addReadGroup(intermediateInBam, intermediateOutBam, readGroup))
index = index - 1
}