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
..
alignment	Disabled AlignerIntegrationTest while addressing build machine memory issues.	2010-08-14 01:23:21 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Add deprecated command-line arguments, and switched over UG to output to	2010-08-22 21:01:44 +00:00
oneoffprojects/walkers	fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!	2010-06-29 21:38:55 +00:00
playground	remove testing code from tribble track builder, set the command line program in walker test to null to reclaim memory in integration tests, and removed some orphaned intergration tests.	2010-08-16 23:52:01 +00:00
utils	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
BaseTest.java	Moving pointer to b36 reference from /broad/1KG to /humgen/1kg	2010-08-13 00:54:34 +00:00
WalkerTest.java	remove testing code from tribble track builder, set the command line program in walker test to null to reclaim memory in integration tests, and removed some orphaned intergration tests.	2010-08-16 23:52:01 +00:00