From 4d6cb33612a1233e17584726cee216526b6ad77c Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Mon, 8 Aug 2011 10:49:28 -0400 Subject: [PATCH] removing temporary bam index The clean bai file was left behind after the data processing pipeline was done --- .../sting/queue/qscripts/DataProcessingPipeline.scala | 1 + 1 file changed, 1 insertion(+) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index 116d16f35..47ba0220f 100755 --- 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