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gatk-3.8/java/test/org/broadinstitute/sting
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hanna 8ff4e4cb25 Cleanup testng listener configuration. 
- Add StingTextReporter, which provides a text dump of the errors to the
  console.  Had to create our own reporter (inheriting from the standard
  TestNG TextReporter) to work around a configuration issue with the
  TextReporter.  In an ideal world, I'd report this on the TestNG mailing
  list and help them resolve the issue, but this solution is relatively
  robust at the moment and life is too short.
- Added back the failed test listener, which generates the testng-failed.xml
  file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4686 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-15 23:43:14 +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 Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
datasources/pipeline Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
gatk VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary 2010-11-15 22:19:22 +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 Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
utils Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. 2010-11-12 20:14:28 +00:00
BaseTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
StingTextReporter.java Cleanup testng listener configuration. 2010-11-15 23:43:14 +00:00
WalkerTest.java New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s 2010-11-13 16:19:56 +00:00