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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AlleleUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeUnitTest.java	Framework for genotype unit test	2011-09-24 08:56:45 -04:00
VCFJarClassLoadingUnitTest.java	Modified the VCFJarClassLoadingUnitTest to play nice with the packaged-jar test targets.	2011-10-25 14:47:15 -04:00
VariantContextBenchmark.java	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
VariantContextUnitTest.java	VariantContextBuilder	2011-11-18 12:39:10 -05:00
VariantContextUtilsUnitTest.java	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
VariantJEXLContextUnitTest.java	ID field now stored in the VariantContext itself, not the attributes	2011-11-15 14:56:33 -05:00