Eric Banks c4ae9c6cfb With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test.		2012-07-29 19:22:02 -04:00
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writer	Allele refactoring checkpoint 2: all code finally compiles, AD and STR annotations are fixed, and most of the UG integration tests pass.	2012-07-26 23:27:11 -04:00
AlleleUnitTest.java	All integration tests and VC/Allele unit tests are passing	2012-07-27 17:03:49 -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	Remove reference dependence in BCF2Codec	2012-07-25 08:56:38 -04:00
VariantContextBenchmark.java	Cleanup Genotypes	2012-06-14 16:42:36 -04:00
VariantContextTestProvider.java	Allele refactoring checkpoint 2: all code finally compiles, AD and STR annotations are fixed, and most of the UG integration tests pass.	2012-07-26 23:27:11 -04:00
VariantContextUnitTest.java	All integration tests and VC/Allele unit tests are passing	2012-07-27 17:03:49 -04:00
VariantContextUtilsUnitTest.java	Final checkpoint: all tests pass. Note that there were bugs in the PoolGenotypeLikelihoodsUnitTest that needed fixing and eventually led to my needing to disable one of the tests (with a note for Guillermo to look into it). Also note that while I have moved over the GATK to use the new non-null representation of Alleles, I didn't remove all of the now-superfluous code throughout to do padding checking on merges; we'll need to do this on a subsequent push.	2012-07-29 01:07:59 -04:00
VariantJEXLContextUnitTest.java	With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test.	2012-07-29 19:22:02 -04:00