6 Commits (304c3e9802d44e52920ee700297e3c92f9fbfdb9)

Author	SHA1	Message	Date
Eric Banks	1fafd9f6c8	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
Eric Banks	d463ab2cbf	BQSR optimization: String manipulation is extremely expensive in Java (accounts for 8% of BQSR runtime). Instead use byte[] and StringBuilder when possible.	2012-06-08 10:42:42 -04:00
Mauricio Carneiro	e89887cd8e	laying groundwork to have insertions and deletions going through the system.	2012-02-07 18:11:53 -05:00
Mauricio Carneiro	b22a3d6508	Functional VCF output. ... It is outputting a VCF with the 'second best guess' for the alternate allele correctly. Annotations are added at the pool level, but may get overwritten at the lane and site level. Still need to implement the merging of the the annotations at higher levels.	2011-08-04 17:49:08 -04:00
Mauricio Carneiro	a58ddab93b	minQual and minPower filters added. VCF output added. ... Calls are now made based on the likelihood AC model. Two filters are applied: minQual and minPower. Output is now a VCF file with the variant context. It's now called the gatk's PoolCaller, no longer Replication Validation framework. Lots of testing ensue....	2011-07-28 18:58:36 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00