gatk-3.8

Author	SHA1	Message	Date
Guillermo del Angel	31c394d588	Resolve merge conflicts	2012-04-18 16:25:03 -04:00
Guillermo del Angel	f9f8589692	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-11 13:56:51 -04:00