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
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	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
test	Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown.	2011-10-19 15:11:13 -04:00