gatk-3.8

Author	SHA1	Message	Date
aaron	c3b2c66911	The GATK doesn't need the rest git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@698 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-14 16:20:45 +00:00
aaron	9f942fdfa0	Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine. Also fixed a bug where we'd exception-out if we didn't provide a interval region. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-12 15:33:55 +00:00
aaron	898f65547e	Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-11 02:07:20 +00:00