gatk3的最后一个经典版本3.8

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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
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00
public	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00
settings	Assorted fixes and improvements to gatkdocs	2014-01-13 17:46:22 -05:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	Separate tests that access the knowledge base from other tests	2013-12-06 11:31:35 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Changing from scala 2.9.2 to 2.10.2.	2013-09-23 12:42:22 -04:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/