David Roazen 02018ca764 Legacy BaseRecalibrator walker is neither TreeReducible nor NanoSchedulable ... The old BaseRecalibrator walker is and never will be thread-safe, since it's a LocusWalker that uses read attributes to track state. ONLY the newer DelocalizedBaseRecalibrator is believed likely to be thread-safe at this point. It is safe to run the DelocalizedBaseRecalibrator with -nct > 1 for testing purposes, but wait for further testing to be done before using it for production purposes in multithreaded mode.		2012-10-24 15:22:50 -04:00
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gatk/walkers	Legacy BaseRecalibrator walker is neither TreeReducible nor NanoSchedulable	2012-10-24 15:22:50 -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