gatk3的最后一个经典版本3.8

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Alec Wysoker 0369f93b24 GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things). 1. Enable on-the-fly indexing for vcf.gz. 2. Handle on-the-fly indexing where file to be indexed is not a regular file, thus index should not be created. 3. Add method setProgressLogger to all SAMFileWriter implementations. 4. Revved picard to 1.109.1722 5. IndelRealigner md5s change because the MC tag is added to records now. Fixed up and signed off by ebanks.		2014-03-17 11:56:22 -04:00
licensing	deleted old license files	2013-07-02 16:36:47 -04:00
protected	GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things).	2014-03-17 11:56:22 -04:00
public	GATK changes to conform to Tribble refactoring as part improving Tabix support in Tribble (among other things).	2014-03-17 11:56:22 -04:00
settings/helpTemplates	Replaced local drmaa and Jama artifacts with versions from maven central.	2014-02-22 01:21:35 +08:00
.gitignore	Adding the external example to the build.	2014-02-15 01:26:07 +08:00
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	Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests	2014-03-10 21:24:03 -04:00

README.md

The Genome Analysis Toolkit

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