Mark DePristo 326f429270 Bugfixes to make new AFCalc system pass integrationtests ... -- GeneralPloidyExactAFCalc turns -Infinity values into -Double.MAX_VALUE, so our calculations pass unit tests -- Bugfix for GeneralPloidyGenotypeLikelihoodsCalculationModel, return a null VC when the only allele we get from our final alleles to use method is the reference base -- Fix calculation of reference posteriors when P(AF == 0) = 0.0 and P(AF == 0) = X for some meaningful value of X. Added unit test to ensure this behavior is correct -- Fix horrible sorting bug in IndependentAllelesDiploidExactAFCalc that applied the theta^N priors in the wrong order. Add contract to ensure this doesn't ever happen again -- Bugfix in GLBasedSampleSelector, where VCs without any polymorphic alleles were being sent to the exact model --		2012-10-21 12:42:31 -04:00
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gatk/walkers	Bugfixes to make new AFCalc system pass integrationtests	2012-10-21 12:42:31 -04:00
utils/pairhmm	Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.	2012-10-20 16:38:18 -04:00