Mark DePristo 2ca5fc62a2 Support for MISSING BCF2 type ... -- Heng wants to use 0x0? to represent any missing type value, which in our implementation was invalid. Updated our codebase to support this construct. Heng said he'll update the BCF2 quick reference. -- Enabled integration test reading Heng's ex2.bcf file -- GATK now only warns in the case where the END info field isn't the same (or +1 due to padding) as the getEnd() function as determined by the GATK. Turns out there's a single record in the 1000G SV call set that doesn't have the right length -- VariantContextTestProvider now tests that X = Y where X -> writing -> reading -> writing -> reading = Y for a variety of variant context inputs X -- Added integration test reading 1000G SV chr1 calls (from Chris)		2012-07-19 16:14:26 -04:00
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writer	Updates to VCF processing for better BCF processing	2012-07-08 15:44:33 -07:00
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	Genotype filters are now just Strings, not Set<String>	2012-06-30 11:22:47 -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	Support for MISSING BCF2 type	2012-07-19 16:14:26 -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