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gatk3的最后一个经典版本3.8
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Valentin Ruano-Rubio 9a9a68409e ReadLikelihoods class introduction final changes before merging 
Stories:

        https://www.pivotaltracker.com/story/show/70222086
        https://www.pivotaltracker.com/story/show/67961652

Changes:

  Done some changes that I missed in relation with making sure that all PairHMM implentations use the same interface; as a consequence we were running always the standard PairHMM.
  Fixed some additional bugs detected when running it on full wgs single sample and exom multi sample data set.
  Updated some integration test md5s.

Fixing GraphBased bugs with new master code
Fixed ReadLikelihoods.changeReads difficult to spot bug.
Changed PairHMM interface to fix a bug
Fixed missing changes for various PairHMM implementations to get them to use the new structure.
Fixed various bugs only detectable when running with full sample(s).
Believe to have fixed the lack of annotations in UG runs
Fixed integrationt test MD5s
Updating some md5s
Fixed yet another md5 probably left out by mistake
 		2014-08-11 17:46:28 -04:00
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected ReadLikelihoods class introduction final changes before merging 2014-08-11 17:46:28 -04:00
public ReadLikelihoods class introduction final changes before merging 2014-08-11 17:46:28 -04:00
settings/helpTemplates Various documentation improvements 2014-07-14 12:03:03 -04:00
.gitignore Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 2014-04-01 16:14:52 -04:00
README.md Update README file for the 2.6 release 2013-06-20 13:08:29 -04:00
ant-bridge.sh Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
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
pom.xml Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00

README.md

The Genome Analysis Toolkit

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