kshakir b954a5a4d5 - 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. ... - More cleanup including removing the temporary classes and intermediate error files. Quieting any errors using Apache Commons IO 2.0. - Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-21 06:37:28 +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	- 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