ebanks 6c739e30e0 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. ... 2. Adding a preliminary version of the new Genotype/Allele interface (putting it into refdata/ as the VariantContext really only applies to rods) with updates to VariantContext. This is by no means complete - further updates coming tomorrow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2533 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-07 05:51:10 +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 is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).	2009-12-16 17:28:09 +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