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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo ccac77d888 Bugfix for incorrect allele counting in IndelSummary 
-- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs
-- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles
-- Update a few pieces of code to get previous correct behavior
-- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct)
-- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default
 		2012-08-01 15:45:12 -04:00
..
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 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 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