Eric Banks 41068b6985 The commit constitutes a major refactoring of the UG as far as the genotype likelihoods are concerned. I hate to do this in stable, but the VCFs currently being produced by the UG are totally busted. I am trying to make just the necessary changes in stable, doing everything else in unstable later. Now all GL calculations are unified into the GenotypeLikelihoods class - please try and use this functionality from now on instead of duplicating the code.		2012-03-15 16:08:58 -04:00
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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	The commit constitutes a major refactoring of the UG as far as the genotype likelihoods are concerned. I hate to do this in stable, but the VCFs currently being produced by the UG are totally busted. I am trying to make just the necessary changes in stable, doing everything else in unstable later. Now all GL calculations are unified into the GenotypeLikelihoods class - please try and use this functionality from now on instead of duplicating the code.	2012-03-15 16:08:58 -04:00
GenotypeUnitTest.java	Change interface to getNegLog10PError to getLog10PError	2011-11-18 21:07:30 -05:00
GenotypesContextUnitTest.java	GenotypesContext now updates cached data for add, set, replace operations when possible	2011-11-22 08:40:48 -05:00
VCFJarClassLoadingUnitTest.java	Modified the VCFJarClassLoadingUnitTest to play nice with the packaged-jar test targets.	2011-10-25 14:47:15 -04:00
VariantContextBenchmark.java	Change interface to getNegLog10PError to getLog10PError	2011-11-18 21:07:30 -05:00
VariantContextUnitTest.java	Bug fix for incorrect logic in subsetSamples	2011-12-14 16:14:26 -05:00
VariantContextUtilsUnitTest.java	Bugfix for pError not being checked correctly in CommonInfo	2011-11-19 15:58:59 -05:00
VariantJEXLContextUnitTest.java	Killing the final versions of old new VariantContext interface	2011-11-18 21:32:43 -05:00