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gatk-3.8/java/test/org/broadinstitute/sting
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kshakir 9923e05e0a Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 
Moved VariantEval validation from FCPTest to PipelineTest.
Cleaned up some duplicate code for writing temp files during tests.
Moved FCPTest to playground namespace to match move for FCP.q.
Added a basic HelloWorldPipelineTest for the HelloWorld QScript. 
Moved duplicated error handling from JobRunners into the FunctionEdge.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5068 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-25 04:11:49 +00:00
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alignment Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
commandline Fixed long-standing bug reported by Mauricio where @Arguments assigned to 2011-01-12 22:18:24 +00:00
datasources/pipeline Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
gatk Fix for Ryan's issue: reads ending with indel distort the location of the 2011-01-24 19:49:39 +00:00
jna For the fullCallingPipeline.q: 2011-01-20 22:34:43 +00:00
oneoffprojects/walkers Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
playground/gatk/walkers Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration. 2011-01-23 05:04:17 +00:00
utils Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 2011-01-25 04:11:49 +00:00
BaseTest.java Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 2011-01-25 04:11:49 +00:00
StingTextReporter.java Cleanup testng listener configuration. 2010-11-15 23:43:14 +00:00
WalkerTest.java Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 2011-01-25 04:11:49 +00:00