gatk3的最后一个经典版本3.8

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Mark DePristo 41aba491c0 Critical bugfix for adapter clipping in HaplotypeCaller -- The previous code would adapter clip before reverting soft clips, so because we only clip the adapter when it's actually aligned (i.e., not in the soft clips) we were actually not removing bases in the adapter unless at least 1 bp of the adapter was aligned to the reference. Terrible. -- Removed the broken logic of determining whether a read adaptor is too long. -- Doesn't require isProperPairFlag to be set for a read to be adapter clipped -- Update integration tests for new adapter clipping code		2013-07-02 15:46:36 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Critical bugfix for adapter clipping in HaplotypeCaller	2013-07-02 15:46:36 -04:00
public	Critical bugfix for adapter clipping in HaplotypeCaller	2013-07-02 15:46:36 -04:00
settings	Rev picard, sam-jdk, tribble, and variant to version 1.91.1453	2013-05-07 14:21:15 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
README.md	Update README file for the 2.6 release	2013-06-20 13:08:29 -04:00
build.xml	Restore scala compilation by default in build.xml	2013-05-31 11:28:29 -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
ivy.xml	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00

README.md

The Genome Analysis Toolkit

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