depristo d9588e6083 bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-09 15:36:12 +00:00
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datasources	LocusIterationByState is now the system deafult. Fixed Aaron's build problem	2009-09-09 01:28:05 +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	General-purpose management of output streams.	2009-08-23 00:56:02 +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	added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option	2009-08-11 22:10:20 +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	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +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