Mark DePristo dcf8af42a8 Finalizing IndependentAllelesDiploidExactAFCalc ... -- Updating integration tests, confirming that results for the original EXACT model are as expected given our new more rigorous application of likelihoods, priors, and posteriors -- Fix basic logic bug in AFCalcResult.isPolymorphic and UnifiedGenotypeEngine, where isNonRef really meant isRef. Not ideal. Finally caught by some tests, but good god it almost made it into the code -- Now takes the Math.abs of the phred-scaled confidence so that we don't see -0.0 -- Massive new suite of unit tests to ensure that bi-allelic and tri-allele events are called properly with all models, and that the IndependentAllelesDiploidExactAFCalc calls events with up to 4 alt alleles correctly. ID'd some of the bugs below -- Fix sort order bug in IndependentAllelesDiploidExactAFCalc caught by new unit tests -- Fix bug in GeneralPloidyExactAFCalc where the AFCalcResult has meaningless values in the likelihoods when no there we no informative GLs.		2012-10-15 08:21:03 -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 IndependentAllelesDiploidExactAFCalc	2012-10-15 08:21:03 -04:00
haplotypecaller	Finalizing IndependentAllelesDiploidExactAFCalc	2012-10-15 08:21:03 -04:00