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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo 2a86b81a3f Initial version of clean, fast formatting routines built dynamically from a VCF header 
-- BCFFieldEncoder and writers divide up the task of formatting values (atomic or vector, ints, strings, floats, etc) from the task of writing these out at the sites or genotypes level.
-- Allows us to create efficient encoders for specific combinations of header fields, such as int[] encoded values with exactly 3 values
-- Currently only used for INFO fields, but subsequent commit will include optimized genotype field encoder
-- Allowed us to naturally support encoding of lists of strings
-- Bugfixes in VariantContextUtils introduced in genotype -> genotypebuilder conversion
-- Fixes for integration test failures
-- Enabling contig updates
-- WalkerTest now prints out relative paths where possible to make cut/paste/run easier
 		2012-06-14 16:42:30 -04:00
..
writer No more makePrecisionFormatStringFromDenominatorValue 2012-06-14 16:42:30 -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 Initial version of clean, fast formatting routines built dynamically from a VCF header 2012-06-14 16:42:30 -04:00
VariantContextUnitTest.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
VariantContextUtilsUnitTest.java Finalizing new Genotype object and associated routines 2012-06-14 16:42:25 -04:00
VariantJEXLContextUnitTest.java Killing the final versions of old new VariantContext interface 2011-11-18 21:32:43 -05:00