gatk-3.8

Author	SHA1	Message	Date
droazen	db9908ec02	Small correction to the unit test code from my last commit. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5572 348d0f76-0448-11de-a6fe-93d51630548a	2011-04-04 18:55:38 +00:00
droazen	a5acb0b7a6	Fix for bug GSA-314: Detect -XL and -L incompatibility. An ArgumentException is now thrown if the combination of -L and -XL intervals specified on the command line results in an empty interval set after set subtraction. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5571 348d0f76-0448-11de-a6fe-93d51630548a	2011-04-04 18:41:55 +00:00
droazen	7b452ea2b9	Fix for bug GSA-430: Can't specify same BAM file twice on the command line. An ArgumentException with an appropriate error message and a list of the duplicate BAMs is now thrown in this case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5542 348d0f76-0448-11de-a6fe-93d51630548a	2011-03-30 22:23:24 +00:00