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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arguments	Removing the obsolete --hapmap and --hapmap_chip options	2010-08-31 16:57:05 +00:00
contexts/variantcontext	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
datasources	Moving StingException	2010-09-12 14:34:15 +00:00
executive	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
filters	Moving StingException	2010-09-12 14:34:15 +00:00
iterators	Eliminated -mrl option.	2010-08-26 21:38:03 +00:00
refdata	Moving StingException	2010-09-12 14:34:15 +00:00
traversals	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
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