gatk3的最后一个经典版本3.8

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Valentin Ruano Rubio 0c25eb7163 Merge pull request #709 from broadinstitute/vrr_fix_general_diploid_exact_af_index_out_of_bounds_bug Fix for the GeneralPloidyExactAFCalc implementation that was preventing -ploidy != 2 GVCF/BP_RESOLUTION output to work. Story: https://www.pivotaltracker.com/story/show/74471252 Tests: Enabled GVCF tests with ploidy != 2 and other checking for the original ArrayIndexOutOfBounds exception.		2014-08-20 16:57:51 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Fixed the bug first by indicating the actual possible number of alternatives alleles considering the extra <NON_REF> and second by resizing the StateTracker capacity when invoked by GeneralPloidyExactAFCalc deep within its implementation of computeLog10PNonRef which is ultimatelly what get rids of the exception.	2014-08-20 14:42:42 -04:00
public	Moving new omniploidy likelihood calculation classes to their final package (as far as this pull-request is concerned) in org.broadinstitute.gatk.tools.walkers.genotyper	2014-08-19 11:54:29 -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/