Mark DePristo 93426a44b1 Fixes for DiagnoseTargets to be VCF/BCF2 spec complaint ... -- Don't use DP for average interval depth but rather AVG_INTERVAL_DP, which is a float now, not an int -- Don't add PASS filter value to genotypes, as this is actually considered failing filters in the GATK. Genotype filters should be empty for PASSing sites		2012-06-28 10:06:05 -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	Fixes for DiagnoseTargets to be VCF/BCF2 spec complaint	2012-06-28 10:06:05 -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