Mark DePristo 669c43031a BCF2 optimizations; parallel CombineVariants ... -- BCF2 now determines whether it can safely write out raw genotype blocks, which is true in the case where the VCF header of the input is a complete, ordered subset of the output header. Added utilities to determine this and extensive unit tests (headerLinesAreOrderedConsistently) -- Cleanup collapseStringList and exploreStringList for new unit tests of BCF2Utils. Fixed bug in edge case that never occurred in practice -- VCFContigHeaderLine now provides its own key (VCFHeader.CONTIG_KEY) directly instead of requiring the user to provide it (and hoping its right) -- More ways to access the data in VCFHeader -- BCF2Writer uses a cache to avoid recomputing unnecessarily whether raw genotype blocks can be emitted directly into the output -- Optimization of fullyDecodeAttributes -- attributes.size() is expensive and unnecessary. We just guess that on average we need ~10 elements for the attribute map -- CombineVariants optimization -- filters are online HashSet but are sorted at the end by creating a TreeSet -- makeCombinations is now makePermutations, and you can request to create the permutations with or without replacement		2012-08-15 21:13:16 -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	BCF2 optimizations; parallel CombineVariants	2012-08-15 21:13:16 -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