gatk3的最后一个经典版本3.8

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Valentin Ruano-Rubio 0e52b8ba5a Fixed MLEAC and QUAL inaccuracy in GeneralPloidyExactAFCalculator. The problem whas that the MLE table calculation aborted "unlikely" genotype combinations to aggresively. This also uncovered another bug where GeneralPloidyExactAFCalculation makes a slightly different use of StateTracker as compared to DiploidExactAFCalculation. We have changed StateTracker generalizing it to be able to work with both using code behaviors. Story: ----- * https://www.pivotaltracker.com/story/show/78920568 Changes: ------- * Fixes in GeneralPloidyExactAFCalculator. * Needed changes in StateTracker API and its consequences in DiploidExactAFCalculation. * Updated affected integrated tests' MD5s after fixing the GeneralPloidyExactAF.		2014-09-23 15:40:54 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Fixed MLEAC and QUAL inaccuracy in GeneralPloidyExactAFCalculator.	2014-09-23 15:40:54 -04:00
public	Added -writeFullFormat engine-level argument	2014-09-17 08:25:27 -04:00
settings/helpTemplates	changed the GATKDocs format to PHP	2014-08-18 18:04:07 -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	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00

README.md

The Genome Analysis Toolkit

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