gatk3的最后一个经典版本3.8

Eric Banks b53336c2d0 Added hidden mode for BQSR to force all read groups to be the same one. ... * Very useful for debugging sample-specific issues * This argument got lost in the transition from BQSR v1 to v2 * Added unit test to cover this case		2013-05-06 19:09:10 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00
public	Merge pull request #208 from broadinstitute/yf_fix_molten_GenotypeConcordance	2013-05-06 08:42:06 -07:00
settings	Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VALUE) when converting from GL to integers. Increase capping to Integer.MAX_VALUE (2^31-1) which should be enough for reasonable sites now. Integration tests change because some tests have some hyper-deep pileups where this case was hit	2013-05-02 16:31:43 -04:00
.gitignore	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
build.xml	Include cofoja jar in classpath when testing release jars	2013-04-30 22:16:58 -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