gatk-3.8

Author	SHA1	Message	Date
hanna	9e2a373184	Prototype, buggy implementation of walker command-line arguments. Doesn't (yet) deal elegantly with even simple cases. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 00:12:00 +00:00
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
hanna	1fcf4c0cbf	Update picard to work with new samtools. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-20 21:51:26 +00:00
aaron	7bc45b68aa	Added dependences on two libraries: the Colt package, which is a collection of high performance computing libraries from CERN; and Log4j, which will be our new logging platform. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@100 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-19 16:16:31 +00:00
hanna	1096bbd4d9	Moved build.xml, ivy.xml and settings to root of Sting repository. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@88 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-18 19:13:19 +00:00