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changed baq to calculate_as_necessary. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5270 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-02-17 23:50:46 +00:00
parent 7f9ca6b28a
commit acad3ada06
1 changed files with 1 additions and 1 deletions
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2
scala/qscript/oneoffs/carneiro/dataProcessing.scala
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@ -152,7 +152,7 @@ class dataProcessing extends QScript {
this.targetIntervals = new File(tIntervals)
this.out = new File(outBam)
this.doNotUseSW = true
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE)
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)