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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
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depristo 2011-04-03 15:35:09 +00:00
parent 5cca100aea
commit 349661b958
1 changed files with 5 additions and 2 deletions
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7
scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala
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@ -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"; })