gatk3的最后一个经典版本3.8

depristo 919a86e876 Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-24 22:32:45 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Changed how the example walker gets run, I'm about to check in the GNU style command line args.	2009-03-22 20:10:17 +00:00
java	Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited...	2009-03-24 22:32:45 +00:00
python	Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.	2009-03-24 03:58:03 +00:00
settings	Update picard to work with new samtools.	2009-03-20 21:51:26 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
build.xml	added some cleanup of code, and new junit targets to the build file	2009-03-24 21:16:12 +00:00
ivy.xml	Switched our code over to the new command line style (gnu style args), added the initial logger code, and added apache commons CLI to the IVY script.	2009-03-22 21:06:22 +00:00