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	4b7bfb284a	Support for more complex command-line types: arrays, untyped collections, typed collections, interfaces to typed and untyped collections. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@194 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-25 20:11:31 +00:00
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
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