From 349661b9587a3a936aba06c788d73ca741c0590e Mon Sep 17 00:00:00 2001 From: depristo Date: Sun, 3 Apr 2011 15:35:09 +0000 Subject: [PATCH] Renamed StratifyAlignmentContext to AlignmentContextUtils, and StatiefyContextType to ReadOrientation. Also, went through the system and deleted all references to second bases. That ship passed long ago. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5563 348d0f76-0448-11de-a6fe-93d51630548a --- .../qscript/oneoffs/depristo/manySampleUGPerformance.scala | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala index 734db13bd..62c88b6b0 100755 --- a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala +++ b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala @@ -53,8 +53,11 @@ class ManySampleUGPerformanceTesting extends QScript { // SNP calling //add(new Call(sublist.list, nSamples, "dynamic_merge")) - val gt = new Call(bams, nSamples, name); - add(gt) + add(new Call(bams, nSamples, name)); + + val gtWithBAQ = new Call(bams, nSamples, name + "_baq"); + gtWithBAQ.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE + add(gtWithBAQ) // SNP calling -- no annotations //add(new Call(bams.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; })