gatk3的最后一个经典版本3.8

aaron 046cecb067 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. ... There will be a slow conversion of all the System.out and System.err in other files to the logger style output. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@145 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-22 21:06:22 +00:00
core/java/src/org/broadinstitute/sting	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
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
playground	Moved to core	2009-03-22 20:02:19 +00:00
settings	Update picard to work with new samtools.	2009-03-20 21:51:26 +00:00
testdata	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
build.xml	Added FourBaseCaller as a jar build target.	2009-03-21 17:59:13 +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