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gatk-3.8/java/test/org/broadinstitute/sting
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kshakir 2ef66af903 Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. 
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-28 23:33:58 +00:00
..
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 Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed. 2011-01-28 23:00:22 +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 the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. 2011-01-28 23:33:58 +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