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removing old GATK options 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5745 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-05-03 21:40:39 +00:00
parent 8bb92160b5
commit c2f8536e02
1 changed files with 0 additions and 1 deletions
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scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
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@ -310,7 +310,6 @@ class dataProcessingV2 extends QScript {
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
// this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
// this.index_output_bam_on_the_fly = true
this.scatterCount = nContigs
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"