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
..
net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	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