Mark DePristo 6b639f51f0 Finalizing new exact model and tests ... -- New capabilities in IndependentAllelesDiploidExactAFCalc to actually apply correct theta^n.alt.allele prior. -- Tests that theta^n.alt.alleles is being applied correctly -- Bugfix: keep in logspace when computing posterior probability in toAFCalcResult in AFCalcResultTracker.java -- Bugfix: use only the alleles used in genotyping when assessing if an allele is polymorphic in a sample in UnifiedGenotyperEngine		2012-10-15 07:53:57 -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	Finalizing new exact model and tests	2012-10-15 07:53:57 -04:00
haplotypecaller	Turning on allele trimming for the haplotype caller.	2012-10-10 10:47:26 -04:00