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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net/sf	GATK tests use public/testdata not /humgen/ as much as possible	2012-05-24 10:58:58 -04:00
org/broadinstitute/sting	First step towards an efficient Genotype object	2012-06-14 16:42:23 -04:00