depristo 2b0d1c52b2 General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-04 19:13:37 +00:00
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datasources	fixed two tests affected by my previous commit	2009-08-11 17:57:50 +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	General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG	2009-09-04 19:13:37 +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