hanna aea121a9d5 <key>=<value> tagging support for command-line arguments. Unfortunately, still ... very hard to validate and still very hard to use (requires core hacking to support additional tags). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-21 00:22:42 +00:00
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GATKArgumentCollection.java	<key>=<value> tagging support for command-line arguments. Unfortunately, still	2011-01-21 00:22:42 +00:00
ValidationExclusion.java	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