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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Mark DePristo ce3d1f89ea ReadShard are no longer allowed to span multiple contigs 
-- Previous behavior was unnecessary and causes all sorts of problems with RODs for reads.  The old implementation simply failed in this case.  The new code handles this correctly by forcing shards to have all of their data on a single contig.
-- Added a PrintReads integration test to ensure this behavior is correct
-- Adding test BAMs that have < 200 reads and span across contig boundaries
 		2012-08-30 10:15:11 -04:00
..
datasources Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers 2012-08-30 10:15:10 -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 WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out). Added another unit test. 2012-08-22 00:24:01 -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 ReadShard are no longer allowed to span multiple contigs 2012-08-30 10:15:11 -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