hanna 01a9b1c63b Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-16 08:33:56 +00:00
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datasources	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +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	an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.	2009-07-23 23:59:48 +00:00
refdata	incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.	2009-09-15 04:48:42 +00:00
traversals	Refactoring of the traversal engine base class, I removed a lot of old code.	2009-07-09 21:57:00 +00:00
walkers	incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.	2009-09-15 04:48:42 +00:00
GATKArgumentCollectionTest.java	Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.	2009-07-08 20:26:16 +00:00