Mark DePristo d37a8a0bc8 Efficient Genotype object Intermediate commit ... -- Created a new Genotype interface with a more limited set of operations -- Old genotype object is now SlowGenotype. New genotype object is FastGenotype. They can be used interchangable -- There's no way to create Genotypes directly any longer. You have to use GenotypeBuilder just like VariantContextBuilder -- Modified lots and lots of code to use GenotypeBuilder -- Added a temporary hidden argument to engine to use FastGenotype by default. Current default is SlowGenotype -- Lots of bug fixes to BCF2 codec and encoder. -- Feature additions -- Now properly handles BCF2 -> BCF2 without decoding or encoding from scratch the BCF2 genotype bytes -- Cleaned up semantics of subContextFromSamples. There's one function that either rederives or not the alleles from the subsetted genotypes -- MASSIVE BUGFIX in SelectVariants. The code has been decoding genotypes always, even if you were not subsetting down samples. Fixed!		2012-06-14 16:42:24 -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	Efficient Genotype object Intermediate commit	2012-06-14 16:42:24 -04:00