Mark DePristo 43ad890fcc Finalizing BCF2 v2 ... -- 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		2012-06-14 16:42:29 -04:00
..
net/sf	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
org/broadinstitute/sting	Finalizing BCF2 v2	2012-06-14 16:42:29 -04:00