hanna 96034aee0e Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered ... that the semantics for which reads are in an extended event pileup are not clear at this point. Eric and I have planned a future clarification for this and the two of us will discuss who will implement this clarification and when it'll happen. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3809 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-16 18:57:58 +00:00
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variantcontext	Add GQ to list of genotype attributes for reg exp	2010-07-14 19:01:11 +00:00
AlignmentContext.java	Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered	2010-07-16 18:57:58 +00:00
ReferenceContext.java	Genotyper now is using bytes not chars. Passes all tests.	2010-05-20 21:02:44 +00:00
StratifiedAlignmentContext.java	An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.	2010-07-07 01:07:46 +00:00