From acad3ada064b2c93fa4f3034eceac9da589b9f56 Mon Sep 17 00:00:00 2001 From: carneiro Date: Thu, 17 Feb 2011 23:50:46 +0000 Subject: [PATCH] changed baq to calculate_as_necessary. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5270 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/oneoffs/carneiro/dataProcessing.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scala/qscript/oneoffs/carneiro/dataProcessing.scala b/scala/qscript/oneoffs/carneiro/dataProcessing.scala index f7b4d1728..8933de5c0 100755 --- a/scala/qscript/oneoffs/carneiro/dataProcessing.scala +++ b/scala/qscript/oneoffs/carneiro/dataProcessing.scala @@ -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)