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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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David Roazen cb84a6473f Downsampling: experimental engine integration 
-Off by default; engine fork isolates new code paths from old code paths,
so no integration tests change yet

-Experimental implementation is currently BROKEN due to a serious issue
involving file spans. No one can/should use the experimental features
until I've patched this issue.

-There are temporarily two independent versions of LocusIteratorByState.
Anyone changing one version should port the change to the other (if possible),
and anyone adding unit tests for one version should add the same unit tests
for the other (again, if possible). This situation will hopefully be extremely
temporary, and last only until the experimental implementation is proven.
 		2012-09-06 15:03:27 -04:00
..
datasources Downsampling: experimental engine integration 2012-09-06 15:03:27 -04:00
downsampling Downsampling: experimental engine integration 2012-09-06 15:03:27 -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 Downsampling: experimental engine integration 2012-09-06 15:03:27 -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 Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig 2012-09-05 21:10:03 -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