Mark DePristo 6bbe750e03 Continuing work on IndependentAllelesDiploidExactAFCalc ... -- Continuing to get IndependentAllelesDiploidExactAFCalc working correctly. A long way towards the right answer now, but still not there -- Restored (but not tested) OriginalDiploidExactAFCalc, the clean diploid O(N) version for Ryan -- MathUtils.normalizeFromLog10 no longer returns -Infinity when kept in log space, enforces the min log10 value there -- New convenience method in VariantContext that looks up the allele index in the alleles		2012-10-15 07:53:56 -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	Continuing work on IndependentAllelesDiploidExactAFCalc	2012-10-15 07:53:56 -04:00
haplotypecaller	Turning on allele trimming for the haplotype caller.	2012-10-10 10:47:26 -04:00