-- Before this branch, the EXACT calculation implementation was largely based on historical choices in the UnifiedGenotyper. The code was badly organized, there were no unit tests, and the Diploid EXACT calculation was super slow O(n.samples ^ n.alt.alleles)
-- Reorganized code into a single class AFCalc superclass that carries out the calculation and an AFCalcResult object that contains only the information we should expose to code users, and is well-validated.
-- Implement a new model for the multi-allelic exact calculation that sweeps for each alt allele B all likelihoods into a bi-allelic model XB where X is all alleles != B, and calls these all separately using the reference bi-allelic model. It produces identical quals for the bi-allelic case but slightly different results for multi-allelics due to a genuine model difference in that this Independent model doesn't penalize fully all genotype configurations as occurs in the Reference multi-allelic implementation. However, it seems after much debate that the reference model is doing the wrong thing, so in fact the Independent model seems correct. This code isn't the default implementation yet, simply because I want to do some cleanup and discuss with the methods group before enabling.
-- Constrained search model implemented, but will be deleted in a subsequent code cleanup
-- Massive (40K) suite of unit tests the exact models, which are passing for the reference and the independent alleles exact model.
-- Restored -- but isn't 100% hooked up -- the original clean bi-allelic model for Ryan to pass his optimized logless version on.
-- The only way to create these AFCalc objects is through an AFCalcFactory, which again validates its arguments. The AFCalcFactory.Calculation enum exposes calculations to the UG / HC as the AFModel.
-- Separated AFCalc from UG, into its own package that could in principle be pushed into utils now
-- Created a simple main[] function to run performance tests of the EXACT model.
57e231610b