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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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depristo 6a30617a60 Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-09 11:32:20 +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 Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 2010-08-25 03:47:57 +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
iterators Eliminated -mrl option. 2010-08-26 21:38:03 +00:00
refdata Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 2010-08-25 03:47:57 +00:00
traversals Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 2010-08-25 03:47:57 +00:00
walkers Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. 2010-09-09 11:32:20 +00:00