Mark DePristo 64d7e93209 Massive bugfixes ... -- Previous version was reading the size of the encoded genotypes vector for each genotype. This only worked because I never wrote out genotype field values with > 15 elements. Mauricio's killer DiagnoseTargets VCF uncovered the bug. Unfortunately since symbolic allele clipping is still busted those tests are still diabled -- GenotypeContext getMaxPloidy was returning -1 in the case where there are no genotypes, but the answer should be 0.		2012-06-28 10:06:06 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Massive bugfixes	2012-06-28 10:06:06 -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