Mark DePristo f54afc19b4 VariantContextBuilder ... -- New approach to making VariantContexts modeled on StringBuilder -- No more modify routines -- use VariantContextBuilder -- Renamed isPolymorphic to isPolymorphicInSamples. Same for mono -- getChromosomeCount -> getCalledChrCount -- Walkers changed to use new VariantContext. Some deprecated new VariantContext calls remain -- VCFCodec now uses optimized cached information to create GenotypesContext.		2011-11-18 12:39:10 -05:00
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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	VariantContextBuilder	2011-11-18 12:39:10 -05:00