Mark DePristo 9b0ab4e941 Cleanup IndependentAllelesDiploidExactAFCalc ... -- Remove capability to truncate genotype likelihoods -- this wasn't used and isn't really useful after all -- Added lots of contracts and docs, still more to come. -- Created a default makeMaxLikelihoods function in ReferenceDiploidExactAFCalc and DiploidExactAFCalc so that multiple subclasses don't just do the default thing -- Generalized reference bi-allelic model in IndependentAllelesDiploidExactAFCalc so that in principle any bi-allelic reference model can be used.		2012-10-16 08:11:06 -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	Cleanup IndependentAllelesDiploidExactAFCalc	2012-10-16 08:11:06 -04:00
haplotypecaller	Increasing the precision of MathUtils.approximateLog10SumLog10 from 1E-3 to 1E-4. Genotyper integration tests change as a result. Expanding the unit tests of MathUtils.log10sumLog10.	2012-10-15 13:24:32 -04:00