delangel a280a0ff0d a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated. ... b) Disabled BaseQualRankSumTest, the returned p-values differ wildly from Matlab/R-provided ones, cause TBD. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3419 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-21 22:25:17 +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	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
datasources	Removing unused methods in QualityUtils; ReferenceContext now converting all bases to upper case, but can be disabled with static boolean	2010-05-20 12:38:06 +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	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
refdata	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
traversals	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
walkers	a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated.	2010-05-21 22:25:17 +00:00