Mark DePristo 0fb8274507 Fix contact on sorting of AFCalcResults ... -- The thing that must be sorted is the pre-theta^N list, which is not checked in the routine that applies the theta^N prior.		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	Fix contact on sorting of AFCalcResults	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