Mark DePristo a648b5e65e First step towards an efficient Genotype object ... -- Created new clean FastGenotype and GenotypeBuilder classes with contracts to enforce expected behavior and correctness. Tested utility of this approach by rewritting -- and then commenting out -- a path in BCF2Codec that could use this new code. Much cleaner interface now, but not yet hooked up to anything -- Disabled SHADOW_BCF generation and generating contigs in the output VCFs automatically to ensure that the current code bases integration tests, before switching the code to new Genotype class -- Code cleanup. Moved "AD" to VCFConstants under GENOTYPE_ALLELIC_DEPTHS. Uses in code replaced with constant		2012-06-14 16:42:23 -04:00
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bcf2	First step towards an efficient Genotype object	2012-06-14 16:42:23 -04:00
beagle	Fixed long-standing bug in beagle codec that was passing on the header record for decoding	2012-05-28 20:17:26 -04:00
hapmap	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
refseq	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
sampileup	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
samread	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
table	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
vcf	First step towards an efficient Genotype object	2012-06-14 16:42:23 -04:00