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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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depristo 116309b3c3 More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4472 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-10-08 20:22:12 +00:00
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arguments Removing the obsolete --hapmap and --hapmap_chip options 2010-08-31 16:57:05 +00:00
contexts/variantcontext Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
datasources Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 2010-09-28 02:16:25 +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 Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
iterators Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
refdata High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file. 2010-10-08 19:53:21 +00:00
traversals Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
walkers More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI 2010-10-08 20:22:12 +00:00
WalkerManagerUnitTest.java Basic unit tests for WalkerManager. 2010-09-30 19:27:41 +00:00