gatk3的最后一个经典版本3.8

Christopher Hartl cd8a6d62bb You know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that. ... This commit contains: - IntronLossGenotyper is brought into its current incarnation - A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate) - RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type. + the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there. - MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added) + use this rather than a hard GQ threshold if you're doing MV analyses. - Some miscellaneous QScripts		2011-10-19 17:42:37 -04:00
public	You know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that.	2011-10-19 17:42:37 -04:00
settings	Merged bug fix from Stable into Unstable	2011-09-27 14:34:39 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Merged bug fix from Stable into Unstable	2011-10-16 07:37:20 -04:00
ivy.xml	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00