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gatk-3.8/public/java/test/org/broadinstitute/sting
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David Roazen 2a7af43164 Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest 
-Some QScripts used by public pipeline tests unnecessarily used the (now protected) UnifiedGenotyper.
 Changed them to use PrintReads instead.

-Moved ExampleUnifiedGenotyperPipelineTest to protected

-Attempt to fix the flawed and sporadically failing MisencodedBaseQualityUnitTest:

   After looking at this class a bit, I think the problem was the use of global arrays for the quals
   shared across all reads in all tests (BAMRecord class definitely does not make a separate copy for
   each read!). One test (testFixBadQuals) modifies the bad quals array, and if this happens to run
   before the testBadQualsThrowsError test the bad quals array will have been "fixed" and no exception
   will be thrown.
 		2013-02-27 04:45:53 -05:00
..
commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk Fix runtime public -> protected dependencies in the test suite 2013-02-26 21:19:12 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest 2013-02-27 04:45:53 -05:00
BaseTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
ExampleToCopyUnitTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
MD5DB.java Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
MD5Mismatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Extend default timeout to 20 minutes 2013-02-13 17:43:40 -08:00
WalkerTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00