From dc8398e165e6dcf138916249d4ce365375008248 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 24 Aug 2011 15:58:34 -0400 Subject: [PATCH] fixing bai output for indel cleaning. --- .../sting/queue/qscripts/DataProcessingPipeline.scala | 1 - 1 file changed, 1 deletion(-) 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 47ba0220f..116d16f35 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -313,7 +313,6 @@ 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