gatk3的最后一个经典版本3.8

Geraldine Van der Auwera d70bf64737 Created new DeprecatedToolChecks class ... --Based on existing code in GenomeAnalysisEngine --Hashmaps hold mapping of deprecated tool name to version number and recommended replacement (if any) --Using FastUtils for maps; specifically Object2ObjectMap but there could be a better type for Strings... --Added user exception for deprecated annotations --Added deprecation check to AnnotationInterfaceManager.validateAnnotations --Run when annotations are initialized --Made annotation sets instead of lists		2013-03-20 06:46:02 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Made some documentation updates & fixes	2013-03-20 06:15:20 -04:00
public	Created new DeprecatedToolChecks class	2013-03-20 06:46:02 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00