gatk3的最后一个经典版本3.8

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Khalid Shakir a894a2dddb Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates. GATK classes accessing package protected htsjdk classes changed to new package names. POMs updated to support merging of sam/tribble/variant -> htsjdk and changes to picard artifact. RodSystemValidation outputs changed due to variant codec packages changes, requiring test md5 updates. Second of four commits for picard/htsjdk package rename.		2014-05-08 19:13:27 +08:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	Add ability to output to a file discordant loci and their respective genotypes for each sample	2014-05-07 10:12:45 -04:00
public	Updates to GATK classes and POMs that need updating, plus RodSystemValidation md5 updates.	2014-05-08 19:13:27 +08:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.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	Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests	2014-03-10 21:24:03 -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	Quoting -out parameter during resource bundle (StingText.properties) creation.	2014-04-15 17:06:49 +08:00

README.md

The Genome Analysis Toolkit

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