Mark DePristo 1f45551a15 Bugfixes to G count types in VCF header ... -- Previously VCF header lines of count type G assumed that the sample would be diploid. -- Generalized the code to take a VariantContext and return the right result for G count types by calling into the correct numGenotypes in GenotypeLikelihoods class -- renamed calcNumGenotypes to numGenotypes, which uses a static cache in the class -- calcNumGenotypes is private, and is used to build the static cache or to compute on the fly for uncached No. allele / ploidy combinations -- VariantContext calls into getMaxPloidy in GenotypesContext, which caches the max ploidy among samples -- Added extensive unit tests that compare A and G type values in genotypes		2012-06-26 15:28:34 -04:00
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writer	BCF2 cleanup	2012-06-26 15:28:33 -04:00
AlleleUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java	Bugfixes to G count types in VCF header	2012-06-26 15:28:34 -04:00
GenotypeUnitTest.java	Cleanup Genotypes	2012-06-14 16:42:36 -04:00
GenotypesContextUnitTest.java	Efficient Genotype object Intermediate commit	2012-06-14 16:42:24 -04:00
VCFJarClassLoadingUnitTest.java	Don't try to share BCF2 yet	2012-05-24 10:57:06 -04:00
VariantContextBenchmark.java	Cleanup Genotypes	2012-06-14 16:42:36 -04:00
VariantContextTestProvider.java	Bugfixes to G count types in VCF header	2012-06-26 15:28:34 -04:00
VariantContextUnitTest.java	Add unit tests for VariantContextBuilder.rmAttribute() and .attribute()	2012-06-25 12:05:04 -04:00
VariantContextUtilsUnitTest.java	Finalizing new Genotype object and associated routines	2012-06-14 16:42:25 -04:00
VariantJEXLContextUnitTest.java	Killing the final versions of old new VariantContext interface	2011-11-18 21:32:43 -05:00