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gatk-3.8/java/test/org/broadinstitute/sting
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depristo f29bb0639b Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5106 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-28 03:40:09 +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 Some basic integration tests detecting breakage in OTF BAM index generation. 2011-01-26 23:48:04 +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 Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory 2011-01-28 03:40:09 +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 Some basic integration tests detecting breakage in OTF BAM index generation. 2011-01-26 23:48:04 +00:00