ebanks b468369dfa -UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one) ... -MQ0 annotation is now standard again -Added AC and AN annotations to VCF output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2545 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-08 05:40:42 +00:00
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AlignmentContext.java	Can now be constructed with either base pileup or extended event (indel) pileup; has query methods checking what kind of pileup is served by the context, and getter methods return the appropriate pileup. TODO: while it is impossible right now to create a context that contains both types of pileups simultaneously, this restriction is only weakly enforced through the lack of appropriate constructor. Either we keep it this way, or some getters may become ambiguous and have to be fixed!	2009-12-29 20:07:29 +00:00
ReferenceContext.java	Renamed ReferenceContext's getSimpleBase() method to getBaseIndex()	2009-12-11 20:14:39 +00:00
StratifiedAlignmentContext.java	-UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one)	2010-01-08 05:40:42 +00:00
VariantContext.java	1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease.	2010-01-07 05:51:10 +00:00