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
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org/broadinstitute/sting/queue	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00
BaseTransitionTableCalculator.scala	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
HelloWorld.scala	support for scala walkers	2009-08-28 00:15:01 +00:00
ScalaCountLoci.scala	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00