carneiro c3f70cc5cb DPP: Updated after some tests with BWA. Still needs more testing. ... MDP: Removed ApplyVariantCut as it's no longer necessary with VQSR2. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5534 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-29 18:22:09 +00:00
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core	DPP: Updated after some tests with BWA. Still needs more testing.	2011-03-29 18:22:09 +00:00
examples	Minor updates to match the wiki documentation.	2011-03-24 20:22:23 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	DPP: Updated after some tests with BWA. Still needs more testing.	2011-03-29 18:22:09 +00:00
playground	Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output.	2011-03-24 14:03:51 +00:00