4 Commits (7ad8fbdd5a98fda65c72974218e500062571ccb4)

Author	SHA1	Message	Date
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	40e6179911	Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-12 14:02:43 +00:00
aaron	30178c05c5	providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3983 348d0f76-0448-11de-a6fe-93d51630548a	2010-08-09 14:00:52 +00:00
asivache	671ac00748	A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3546 348d0f76-0448-11de-a6fe-93d51630548a	2010-06-14 15:54:37 +00:00