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ebanks ca5b274f16 Unit, integration, and performance tests are all busted, so this is a good time to make a big commit... 
Major cleanup of the genotype writer code from the calling end.  UG no longer supports making calls in anything but VCF, and that allows us to use the VCFWriter more generically now.  Putting the ball in Matt's court to finish collapsing everything.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3996 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-10 04:18:29 +00:00
..
arguments fixes for the Tree index, and some small clean-up in the GATK. 2010-08-09 20:41:50 +00:00
contexts/variantcontext VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include: 2010-08-05 18:47:53 +00:00
datasources Removed hard-coded pointers to references 2010-08-04 17:59:37 +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 Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
refdata Unit, integration, and performance tests are all busted, so this is a good time to make a big commit... 2010-08-10 04:18:29 +00:00
traversals IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. 2010-07-01 04:40:31 +00:00
walkers Unit, integration, and performance tests are all busted, so this is a good time to make a big commit... 2010-08-10 04:18:29 +00:00