gatk-3.8

Author	SHA1	Message	Date
droazen	d650efd40a	Fix for bug GSA-449: Intervals that are not in GATK format are not validated to the same standard as GATK format intervals. Full validation against contig bounds is now performed for all intervals, regardless of their source. Also fixed a few tests for validation exclusions that were backwards. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5698 348d0f76-0448-11de-a6fe-93d51630548a	2011-04-27 18:12:10 +00:00
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