gatk-3.8

Author	SHA1	Message	Date
hanna	53fe9acf65	Make command-line arguments available in walker constructor, provide back door from walker into GATK itself, do some cleanup of output messages, and add some bug fixes. Command-line arguments in walkers are now feature-complete, but still a bit messy. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-26 20:45:27 +00:00
hanna	5f9010116a	Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-26 16:22:35 +00:00
depristo	8bdf49a01f	added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 03:12:54 +00:00
hanna	63cd1fe201	Push core / playground lower into the tree. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-23 23:19:54 +00:00