4 Commits (fa8cfd30319badb83cf7f2ac08b607e594ccb89a)

Author	SHA1	Message	Date
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
hanna	bf0b6bd486	Update integration tests to use the new ROD syntax. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4112 348d0f76-0448-11de-a6fe-93d51630548a	2010-08-25 18:13:30 +00:00
hanna	0490909285	Fixed epic generic paths fail. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3359 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-13 15:59:57 +00:00
hanna	7ef87e5126	An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less ... than a minute and fell over instantly in the case of the Tribble parallelism issue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-13 15:40:43 +00:00