Mark DePristo 695cf83675 More docs and contracts for classes in genotyper.afcalc ... -- Future protection of the output of GeneralPloidyExactAFCalc, which produces in some cases bad likelihoods (positive values)		2012-10-21 12:42:31 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	More docs and contracts for classes in genotyper.afcalc	2012-10-21 12:42:31 -04:00
test	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