kshakir fd5970fdd4 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. ... No longer generating deprecated GATK arguments on the Queue extensions. Emitting deprecation warnings to Queue compile to help debugging issues. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-02 21:30:48 +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	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