kshakir 2ef66af903 Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. ... Moved the BamListWriter from FCP to ListWriterFunction in the Queue core. Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s. Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-28 23:33:58 +00:00
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ExampleCountLoci.scala	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
ExampleCountReads.scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
ExampleCustomWalker.scala	Allowing the Queue to run the GATK via -cp instead of only from -jar.	2010-08-27 16:25:59 +00:00
ExampleUnifiedGenotyper.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
HelloWorld.scala	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +00:00