Mark DePristo 13211231c7 Restructure and cleanup ExactAFCalculations ... -- Now there's no duplication between exact old and constrained models. The behavior is controlled by an overloaded abstract function -- No more static function to access the linear exact model -- you have to create the surrounding class. Updated code in the system -- Everything passes unit tests		2012-10-15 07:53:54 -04:00
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bqsr	updating BQSR integration tests	2012-09-19 14:10:34 -04:00
compression/reducereads	Refactored the BaseCounts classes so that they are safer and allow for calculations on the most probable base (which is not necessarily the most common base).	2012-10-04 10:37:11 -04:00
genotyper	Restructure and cleanup ExactAFCalculations	2012-10-15 07:53:54 -04:00
haplotypecaller	Turning on allele trimming for the haplotype caller.	2012-10-10 10:47:26 -04:00