hanna 8f75d88519 Fix for GATK run report ids: ... mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ 8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf iLhvHWveypKb2F8vKS5irHylc3pYvlOb HDttXKUMEVoPrvVeWrH7E0htxYyNydMx plus a bit of cleanup of custom exceptions in the sharding system. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4330 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-22 19:49:25 +00:00
..
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	Fix for GATK run report ids:	2010-09-22 19:49:25 +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	Eliminated -mrl option.	2010-08-26 21:38:03 +00:00
refdata	one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry.	2010-09-21 18:47:20 +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	Disable VCF header output in the Beagle integrationtest.	2010-09-22 16:50:03 +00:00