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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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David Roazen 2eac97a76c Remove auto-creation of fai/dict files for fasta references 
-A UserException is now thrown if either the fai or dict file for the
 reference does not exist, with pointers to instructions for creating
 these files.

-Gets rid of problematic file locking that was causing intermittent
 errors on our farm.

-Integration tests to verify that correct exceptions are thrown in
 the case of a missing fai / dict file.

GSA-866 #resolve
 		2013-04-02 18:34:08 -04:00
..
datasources Remove auto-creation of fai/dict files for fasta references 2013-04-02 18:34:08 -04:00
downsampling - Changed loadContaminationFile file parser to delimit by tab only. This allows spaces in sampleIDs, which apparently are allowed. 2013-03-07 13:04:24 -05:00
executive Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Added check in the MalformedReadFilter for reads without stored bases (i.e. that use '*'). 2013-03-14 17:17:26 -04:00
iterators Refactor LIBS into utils.locusiterator before refactoring 2013-01-11 15:17:16 -05:00
refdata Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
samples Updating TestNG to the latest version 2013-02-22 09:40:23 -05:00
traversals Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
walkers Refactored the het (polyploid) consensus creation in ReduceReads. 2013-03-25 09:34:54 -04:00
CommandLineGATKUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java Further tweaking of test timeouts 2013-03-15 14:49:21 -04:00
GenomeAnalysisEngineUnitTest.java Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine. 2013-03-06 12:38:59 -05:00
MaxRuntimeIntegrationTest.java Bump timeout for MaxRuntimeIntegrationTest 2013-03-17 16:17:29 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00