Ernesto Brau e8b42c4dfd Use GKL's implementation of Vector Logless Pair HMM ... Fixed MuTect2 tests by removing old -alwaysloadVectorHmm flag; upgraded to GKL 0.5.2; FASTEST_AVAILABLE pairhmm option; improved documenting comments in code Made FASTEST_AVAIALABLE the default for the pairHMM cmdline argument Make LOGLESS_CACHING the default pairHMM unified cmdline argument, fix error message if choose an unrecognized pairHMM Updae MD5s		2017-06-07 13:33:32 -04:00
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src	Changed calculation of rank sum so it's now the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics). Now only called alt for 0/1s has rank sum, similar to old paradigm. Combined gVCF rank sums stored in Histogram, then median is taken once during genotyping. Histogram uses Integer keys to eliminate numerical precision mess	2017-05-10 09:04:42 -04:00
pom.xml	Use GKL's implementation of Vector Logless Pair HMM	2017-06-07 13:33:32 -04:00