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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collections	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00
genotyper	Relaxing the constraints on the readIsPoorlyModelled function.	2013-06-13 11:06:23 -04:00
gvcf	Bugfix for hom ref records that aren't GVCF blocks.	2013-09-29 19:19:26 -04:00
haplotype	Better caching for the HaplotypeCaller	2013-08-02 01:27:29 -04:00
haplotypeBAMWriter	Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences	2013-07-02 15:46:38 -04:00
nanoScheduler	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00
pairhmm	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00
recalibration	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00
smithwaterman	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00
ContigComparatorUnitTest.java	Generalize and fixup ContigComparator	2013-02-09 09:52:13 -05:00
RandomDNA.java	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00