ebanks 0dd65461a1 Various improvements to plink, variant context, and VCF code. ... We almost completely support indels. Not yet done with plink stuff. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-04 17:58:01 +00:00
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arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
contexts/variantcontext	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
datasources	a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.	2010-03-03 16:31:45 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach).	2010-02-02 23:13:10 +00:00
refdata	a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.	2010-03-03 16:31:45 +00:00
traversals	Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a	2010-02-25 00:16:50 +00:00
walkers	Various improvements to plink, variant context, and VCF code.	2010-03-04 17:58:01 +00:00