kshakir 673fa841a4 Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. ... Removed obsolete usages of PackageUtils with updated PluginManager. Ported Queue interval utilities written in scala over to Sting's java IntervalUtils. Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles. Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test). While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1". Upgraded to scala 2.8.1 and updated calls to deprecated functions. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-12 20:14:28 +00:00
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org/broadinstitute/sting/queue	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +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