depristo 595907e98e Moving StingException ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-12 14:34:15 +00:00
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alignment	all fixed..thanks Matt!	2010-09-10 06:18:59 +00:00
commandline	Moving StingException	2010-09-12 14:34:15 +00:00
gatk	Moving StingException	2010-09-12 14:34:15 +00:00
oneoffprojects/walkers	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.	2010-09-12 14:02:43 +00:00
playground	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
utils	Moving StingException	2010-09-12 14:34:15 +00:00
BaseTest.java	Moving StingException	2010-09-12 14:34:15 +00:00
WalkerTest.java	Moving StingException	2010-09-12 14:34:15 +00:00