gatk-3.8

Author	SHA1	Message	Date
aaron	d115209e86	moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@209 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-27 13:27:04 +00:00
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	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	f7363cf935	Support for loading from either a jar or a class directory. Fixes troubles with IntelliJ debugging. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@162 348d0f76-0448-11de-a6fe-93d51630548a	2009-03-24 03:56:49 +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