Mark DePristo be3230a1fd Initial implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates ... -- Created makeCombinations utility function (very useful!). Moved template from VariantContextTestProvider -- UnitTests for basic functionality		2012-08-15 21:13:15 -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	Bugfix for incorrect allele counting in IndelSummary	2012-08-01 15:45:12 -04:00
VariantContextTestProvider.java	Initial implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates	2012-08-15 21:13:15 -04:00
VariantContextUnitTest.java	All integration tests and VC/Allele unit tests are passing	2012-07-27 17:03:49 -04:00
VariantContextUtilsUnitTest.java	Re-enabling the unit tests for reverse allele clipping	2012-07-29 22:24:56 -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