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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo d37a8a0bc8 Efficient Genotype object Intermediate commit 
-- Created a new Genotype interface with a more limited set of operations
-- Old genotype object is now SlowGenotype.  New genotype object is FastGenotype.  They can be used interchangable
-- There's no way to create Genotypes directly any longer.  You have to use GenotypeBuilder just like VariantContextBuilder
-- Modified lots and lots of code to use GenotypeBuilder
-- Added a temporary hidden argument to engine to use FastGenotype by default.  Current default is SlowGenotype
-- Lots of bug fixes to BCF2 codec and encoder.
-- Feature additions
  -- Now properly handles BCF2 -> BCF2 without decoding or encoding from scratch the BCF2 genotype bytes
  -- Cleaned up semantics of subContextFromSamples.  There's one function that either rederives or not the alleles from the subsetted genotypes

-- MASSIVE BUGFIX in SelectVariants.  The code has been decoding genotypes always, even if you were not subsetting down samples.  Fixed!
 		2012-06-14 16:42:24 -04:00
..
writer Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
AlleleUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
GenotypeUnitTest.java Change interface to getNegLog10PError to getLog10PError 2011-11-18 21:07:30 -05:00
GenotypesContextUnitTest.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
VCFJarClassLoadingUnitTest.java Don't try to share BCF2 yet 2012-05-24 10:57:06 -04:00
VariantContextBenchmark.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
VariantContextTestProvider.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
VariantContextUnitTest.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
VariantContextUtilsUnitTest.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
VariantJEXLContextUnitTest.java Killing the final versions of old new VariantContext interface 2011-11-18 21:32:43 -05:00