43ad890fcc
-- FastGenotypes are the default in the engine. Use --useSlowGenotypes engine argument to return to old representation
-- Cleanup of BCF2Codec. Good error handling. Added contracts and docs.
-- Added a few more contacts and docs to BCF2Decoder
-- Optimized encodePrimitive in BCF2Encoder
-- Removed genotype filter field exceptions
-- Docs and cleanup of BCF2GenotypeFieldDecoders
-- Deleted unused BCF2TestWalker
-- Docs and cleanup of BCF2Types
-- Faster version of decodeInts in VCFCodec
-- BCF2Writer
-- Support for writing a sites only file
-- Lots of TODOs for future optimizations
-- Removed lack of filter field support
-- No longer uses the alleleMap from VCFWriter, which was a Allele -> String, now uses Allele -> Integer which is faster and more natural
-- Lots of docs and contracts
-- Docs for GenotypeBuilder. More filter creation routines (unfiltered, for example)
-- More extensive tests in VariantContextTestProfiler, including variable length strings in genotypes and genotype filters. Better genotype comparisons
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|---|---|---|
| .. | ||
| writer | ||
| AlleleUnitTest.java | ||
| GenotypeLikelihoodsUnitTest.java | ||
| GenotypeUnitTest.java | ||
| GenotypesContextUnitTest.java | ||
| VCFJarClassLoadingUnitTest.java | ||
| VariantContextBenchmark.java | ||
| VariantContextTestProvider.java | ||
| VariantContextUnitTest.java | ||
| VariantContextUtilsUnitTest.java | ||
| VariantJEXLContextUnitTest.java | ||