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
..
HLAcaller	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
annotator	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
duplicates	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00
poolseq	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
validation	adding tests for BTI in the ROD validation tests	2010-08-10 06:05:40 +00:00
vcftools	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
BeagleIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
ClipReadsWalkersIntegrationTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00