Merged bug fix from Stable into Unstable

2011-08-08 10:50:09 -04:00 · 2011-08-08 10:50:09 -04:00 · 0db46d0648
parent 88061ed5fa 2fd101135c
commit 0db46d0648
1 changed files with 1 additions and 0 deletions
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@ -313,6 +313,7 @@ class DataProcessingPipeline extends QScript {
  }

  case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
+    @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai")
    this.input_file :+= inBams
    this.targetIntervals = tIntervals
    this.out = outBam