kshakir 88a0d77433 Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines. ... Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator. Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered. Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers. Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-20 21:43:52 +00:00
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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	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.	2010-10-20 21:43:52 +00:00