Eric Banks 41f3da75d7 Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.		2011-08-12 02:22:44 -04:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.	2011-08-12 02:22:44 -04:00