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
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gatk	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.	2009-05-11 02:07:20 +00:00
utils	Started the process to make the GATK engine into a runnable object so we can call it from other processes. Step 1: make a configuration object that can serialize to and from an XML file. This way we can store the information everyone uses shell scripts for. Also we can now pull the list of params out of the GenomeAnalysisTK.java. More to come...	2009-05-08 01:25:26 +00:00
BaseTest.java	Added BCEL and some basic instrumenation code to the test library.	2009-05-06 17:18:23 +00:00
TrivialInstrumenter.java	Added BCEL and some basic instrumenation code to the test library.	2009-05-06 17:18:23 +00:00