4 Commits (960e7e6aaf1e1ed46d7ee6b6d59802ca8eba716c)

Author	SHA1	Message	Date
Guillermo del Angel	c78b0eee3a	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.	2012-04-17 14:22:48 -04:00
Mauricio Carneiro	1b75663178	BQSR Gatherer implementation and integration tests ... * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration	2012-03-27 13:50:22 -05:00
Ryan Poplin	0c6b34e9df	Fixing a bug identified by the ActivityProfile unit tests	2012-03-15 14:24:30 -04:00
Mark DePristo	7c5cdb51c2	UnitTests for ActivityProfile and minor ART cleanup ... -- TODO for ryan -- there are bugs in ActivityProfile code that I cannot fix right now :-( -- UnitTesting framework for ActivityProfile -- needs to be expanded -- Minor helper functions for ActiveRegion to help with unit tests	2012-03-14 17:26:37 -04:00