Eric Banks be9e48ba29 Merged bug fix from Stable into Unstable		2012-03-16 14:33:53 -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	Add a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing.	2012-03-16 11:14:37 -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	Adding contracts and unit tests for HaplotypeCaller GenotypingEngine	2012-03-15 11:55:48 -04:00
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