kshakir f39dce1082 Exposed CommandLineFunction defaults to the Queue.jar command line (see -help). ... Added ability to skip up-to-date jobs where the outputs are older than the inputs. Changed -T CountDuplicates --quiet to --quietLocus so that Queue GATK extensions can use both short and full argument names. Short names can be used to set values on Queue GATK extensions, for example: vf.XL :+= myFile Moved Hidden from the GATK to StingUtils. Updated ivy from 2.0.0 to 2.2.0-rc1 to fix sha1 issue: http://bit.ly/aX72w7 Added Queue to javadoc and testing build targets. Added first Queue unit test. Another pass at avoiding cycles in the DAG thanks to all function I/O being files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4017 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-11 21:58:26 +00:00
..
alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +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	Massive cleanup of read filtering.	2010-08-11 20:17:11 +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	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00
utils	providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.	2010-08-09 14:00:52 +00:00
BaseTest.java	adding tests for BTI in the ROD validation tests	2010-08-10 06:05:40 +00:00
WalkerTest.java	fix for feature source in Tribble; we need to check that the record coming back isn't null. Also in the GATK added code to set the default logging level in integration tests to WARN, with the default level change they were spewing a bunch of text.	2010-08-10 02:57:23 +00:00