Mark DePristo cf3f9d6ee8 Reorganize and cleanup AFCalculations ... -- Now contained in a package called afcalc -- Extracted standard alone classes from private static classes in ExactAF -- Most fields are now private, with accessors -- Overall cleaner organization now		2012-10-15 07:53:55 -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	Reorganize and cleanup AFCalculations	2012-10-15 07:53:55 -04:00
haplotypecaller	Turning on allele trimming for the haplotype caller.	2012-10-10 10:47:26 -04:00