ebanks 2307bed742 VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E). ... Generalized some of the packaging code from VariantAnnotator. Matt might want to take a look to make this nicer...? git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3925 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-03 16:51:10 +00:00
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arguments	Experimental versions of downsampler and Ryan's deduper are now available either	2010-05-19 05:40:05 +00:00
contexts/variantcontext	a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...	2010-07-22 02:36:45 +00:00
datasources	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
executive	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
filters	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
io	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
iterators	Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered	2010-07-16 18:57:58 +00:00
refdata	updates to code dependent on Tribble, as well as the following Tribble changes:	2010-07-23 01:56:10 +00:00
traversals	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
walkers	VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E).	2010-08-03 16:51:10 +00:00