ebanks 4678613893 Significant fixes for the Genomic Annotator. ... 1. Rip out all of Ben's code intended to circumvent the stable VCF Writer output system in multi-threaded mode (I threw up a little when I saw this code). This will improve memory consumption when running with -nt. 2. Don't annotate indels or > bi-allelic sites. 3. Fix bug where not all records were making it into the output VCF. 4. General code clean up. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4118 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-25 20:16:50 +00:00
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HLAcaller	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
annotator	Significant fixes for the Genomic Annotator.	2010-08-25 20:16:50 +00:00
duplicates	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00
poolseq	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
validation	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
BeagleIntegrationTest.java	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
ClipReadsWalkersIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00