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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects 
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous.  Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
 		2011-11-11 15:00:35 -05:00
..
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 More general handling of parameters for VariantContextBenchmark 2011-11-11 10:22:19 -05:00
VariantContextIntegrationTest.java More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track. 2011-08-10 14:24:40 -04:00
VariantContextUnitTest.java Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown. 2011-10-19 15:11:13 -04:00
VariantContextUtilsUnitTest.java VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -05:00
VariantJEXLContextUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00