Mark DePristo 17fbd103d0 Smarter infrastructure to decode genotypes in BCF ... -- Eliminated the large intermediate map from field name to list of list<Integer> values needed to create genotypes without the GenotypeBuilder. The new code is cleaner and simply fills in an array of GenotypeBuilders as it moves through the column layout in BCF2 -- Now we create once decoders specialized for each GT field (GT, AD, etc) that can be optimized for putting data into the GenotypeBuilder. In a subsequent commit these will actually use lower level BCF2 decoders to create the low-level ints and int[], avoiding the intermediate List<Integer> form -- Reduced the amount of data further to be computed in the DiffEngine. The DiffEngine algorithm needs to be rethought to be efficient...		2012-06-14 16:42:25 -04:00
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sting	Smarter infrastructure to decode genotypes in BCF	2012-06-14 16:42:25 -04:00