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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Eric Banks dce6b91f7d 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
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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 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