Valentin Ruano-Rubio 9e7bf75e89 Fix for the PairHMM transition probability miscalculation. ... Problem: matchToMatch transition calculation was wrong resulting in transition probabilites coming out of the Match state that added more than 1. Reports: https://www.pivotaltracker.com/s/projects/793457/stories/62471780 https://www.pivotaltracker.com/s/projects/793457/stories/61082450 Changes: The transition matrix update code has been moved to a common place in PairHMMModel to dry out its multiple copies. MatchToMatch transtion calculation has been fixed and implemented in PairHMMModel. Affected integration test md5 have been updated, there were no differences in GT fields and example differences always implied small changes in likelihoods that is what is expected.		2014-01-26 16:30:36 -05:00
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net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00