gatk-3.8

Author	SHA1	Message	Date
hanna	862b8a6787	intervals_file + genome_loc => intervals. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@659 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-12 01:04:18 +00:00
aaron	ff1b92acc4	Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-11 22:05:58 +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