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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Mark DePristo 0892f2b8b2 Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference 
-- Confirmed that reads spanning off the end of the chromosome don't cause an exception by adding integration test for a single read that starts 7 bases from the end of chromosome 1 and spans 90 bases or so off.  Added pileup integration test to ensure this behavior continues to work
 		2012-09-03 20:18:56 -04:00
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datasources Fix build problems with tests 2012-08-31 13:42:41 -04:00
downsampling Make downsampler classes themselves generic (instead of just the Downsampler interface) 2012-06-13 16:43:39 -04:00
executive Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters Updated and more thorough version of the BadCigar read filter 2012-08-17 17:05:27 -04:00
iterators Fix build problems with tests 2012-08-31 13:42:41 -04:00
refdata Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers 2012-08-30 10:15:10 -04:00
report Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
samples Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
traversals Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00
walkers Closing GSA-287:LocusReferenceView doesn't do very well in the case where contigs land off the end of the reference 2012-09-03 20:18:56 -04:00
CommandLineGATKUnitTest.java Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us. 2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java Sorting out HMS error handling (fingers crossed) 2012-07-25 23:13:12 -04:00
GenomeAnalysisEngineUnitTest.java Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java Fixing walker unit test with the new naming convention 2012-07-20 17:50:29 -04:00