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
..
R	Fixing errors in queueJobReport runtime unit	2011-10-07 12:04:53 -07:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	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
packages	Enable testing of the jars produced by the packaging system.	2011-10-14 03:08:28 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-10-18 15:23:05 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00