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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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ebanks c6ad26e04f 1) When quals/GQs are really integers (x.00), strip off the floating points. 
2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID.  Use a static variable instead.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-20 18:01:45 +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 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +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 re-enable test; I was moving the input file in prep for my last commit around on Eric, so he rightfully removed the test 2010-07-20 07:14:59 +00:00
traversals IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. 2010-07-01 04:40:31 +00:00
walkers 1) When quals/GQs are really integers (x.00), strip off the floating points. 2010-07-20 18:01:45 +00:00