gatk3的最后一个经典版本3.8

Mark DePristo 73a363b166 Update MD5s due to new QualityUtils calculations ... -- Increase the allowed runtime of one UG integration test -- The GGA indels mode runs two UG commands, and was barely under the 10 minute limit before. Some updates can push this right over the edge. Increased limit -- CalibrateGenotypeLikelihoods runs on a small data set now, so it's faster -- Updating MD5s due to more correct quality utils. DuplicatesWalkers quality estimates have changed. One UG test has different FS and rank sum tests because the conversion to phred scores are slightly (second decimal place) different		2013-02-16 07:31:38 -08:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected/java	Update MD5s due to new QualityUtils calculations	2013-02-16 07:31:38 -08:00
public	Final edge case bug fixes to QualityUtil routines	2013-02-16 07:31:38 -08:00
settings	Refactored GATKDocs categories some more ( GSATDG-62 )	2013-02-13 16:49:18 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Minor build.xml cleanup post-variant-migration	2013-02-06 11:16:52 -05:00
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	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00