David Roazen 35483a7eef Update MD5s for PrintReads with BQSR Integration Test ... The MD5s for these tests were changed in commit 87435f1074615b2cd016f042980109fd53962c8d to match the output of a broken version of BaseRecalibration. With the patch in commit c397102ecc1fd1d2cd8f209a8f358ab4a60b50a7, the output once again matches the *original* MD5s for these tests, and does not vary as you increase -nct. Final resolution to GSA-632		2012-10-26 14:25:25 -04:00
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gatk/walkers	Update MD5s for PrintReads with BQSR Integration Test	2012-10-26 14:25:25 -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