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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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
scala	Merge remote-tracking branch 'origin/master' into mf_new_RBP	2013-12-19 10:42:20 -05:00
testdata	Fixed up and refactored what seems to be a useful private tool to create simulated reads around a VCF.	2014-01-15 13:49:31 -05:00