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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Eric Banks 3759d9dd67 Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine. 
* ReadTransformers can say they must be first, must be last, or don't care.
  * By default, none of the existing ones care about ordering except BQSR (must be first).
    * This addresses a bug reported on the forum where BAQ is incorrectly applied before BQSR.
  * The engine now orders the read transformers up front before applying iterators.
  * The engine checks for enabled RTs that are not compatible (e.g. both must be first) and blows up (gracefully).
  * Added unit tests.
 		2013-03-06 12:38:59 -05:00
..
datasources Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
downsampling Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
executive Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Added better error message for BAMs with bad read groups. 2013-02-27 16:02:56 -05:00
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 Collapse the downsampling fork in the GATK engine 2013-01-28 01:50:30 -05:00
walkers Fix runtime public -> protected dependencies in the test suite 2013-02-26 21:19:12 -05:00
CommandLineGATKUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java Fix runtime public -> protected dependencies in the test suite 2013-02-26 21:19:12 -05:00
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 Fix runtime public -> protected dependencies in the test suite 2013-02-26 21:19:12 -05:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00