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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broadinstitute/sting	Bugfixes to make new AFCalc system pass integrationtests	2012-10-21 12:42:31 -04:00