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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo 91f3204534 VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself 
-- Turns out this was consuming 30% of the UG runtime, and causing problems elsewhere.
-- Removed addMissingSamples from VariantcontextUtils, and calls to it
-- Updated VCF / BCF writers to automatically write out a diploid no call for missing samples
-- Added unit tests for this behavior in VariantContextWritersUnitTest
 		2012-09-12 06:46:26 -04:00
..
writer VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself 2012-09-12 06:46:26 -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 VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself 2012-09-12 06:46:26 -04:00
VariantContextUnitTest.java Using the simple VCBuilder constructor and then subsequently trying to modify attributes was throwing a NPE. This is easily solved (without a performance hit) by initializing the attributes map to an immutable Collections.emptyMap(). Added unit test to cover this case. 2012-08-22 12:54:29 -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