gatk-3.8

Author	SHA1	Message	Date
depristo	6a30617a60	Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-09 11:32:20 +00:00
hanna	c1e53d407d	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had unicode quote characters embedded in it. These characters were invisible inside IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason have a different default charset. Fixed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-20 15:26:32 +00:00
hanna	1bc26f69e9	An attempt to cleanup the Utils directory. Email to follow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-19 23:00:08 +00:00