hanna c177801d81 Add deprecated command-line arguments, and switched over UG to output to ... -o/--out instead of -varout. Let's watch as our intrepid support engineer gracefully responds to all the incoming questions of the form: "the GATK told me to use -o instead of -varout. What do I do?" git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4078 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-22 21:01:44 +00:00
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arguments	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
contexts/variantcontext	moving tests over from the GATK to Tribble, and added a speed-up to the readNextRecord() that Mark suggested. Also removed the contained flag from the queries to Tribble in the GATK.	2010-08-10 17:54:59 +00:00
datasources	Massive cleanup of read filtering.	2010-08-11 20:17:11 +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	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
refdata	remove some dependencies on out of date methods from the tests	2010-08-17 00:07:26 +00:00
traversals	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
walkers	Add deprecated command-line arguments, and switched over UG to output to	2010-08-22 21:01:44 +00:00