gatk-3.8

Author	SHA1	Message	Date
depristo	7880863eb7	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-12 15:07:38 +00:00
depristo	7ad8fbdd5a	Moved GATKException to exceptions git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-12 14:47:19 +00:00
depristo	8f1a32acae	All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-10 15:25:30 +00:00
hanna	6e60cddfed	A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu e. Really a stopgap; error handling in the RODs needs to be addressed in a more comprehensive way. Right now, hasNext() isn't guaranteed to be correct. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@878 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-02 18:14:46 +00:00