aaron d8fedd59be docs, cleanup, and some improvements to the iterators. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-26 22:36:04 +00:00
..
arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
contexts/variantcontext	Support for no qual fields in VCF; better support for Mendelian violation calculations	2010-02-26 00:29:17 +00:00
datasources	RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.	2010-02-25 22:48:55 +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	docs, cleanup, and some improvements to the iterators.	2010-02-26 22:36:04 +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	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