Eric Banks dc7636b923 Refactor the ContextCovariate to significantly reduce runtime		2012-06-28 02:29:35 -04:00
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src	Refactor the ContextCovariate to significantly reduce runtime	2012-06-28 02:29:35 -04:00
test	NestedHashMap-based implementation of BQSRv2 along with a few minor optimizations. Not a huge runtime upgrade over the long bitset approach, but it allows us to implement further optimizations going forward. Integration test change because the original version had a bug in the quantized qual table creation.	2012-06-27 16:55:49 -04:00