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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Christopher Hartl 1be8a88909 Changes: 
1) GATKArgumentCollection has a command to turn off randomization if setting the seed isn't enough. Right now it's only hooked into RankSumTest.
 2) RankSumTest now can be passed a boolean telling it whether to use a dithering or non-randomizing comparator. Unit tested.
 3) VariantsToBinaryPed can now output in both individual-major and SNP-major mode. Integration test.
 4) Updates to PlinkBed-handling python scripts and utilities.
 5) Tool for calculating (LD-corrected) GRMs put under version control. This is analysis for T2D, but I don't want to lose it should something happen to my computer.
 		2012-10-03 16:02:42 -04:00
..
datasources ExperimentalReadShardBalancerUnitTest was being skipped; fixed 2012-09-22 01:56:39 -04:00
downsampling Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -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 Experimental, downsampler-friendly read shard balancer 2012-09-21 22:17:58 -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 Refactor TraversalEngine to extract the progress meter functions 2012-09-10 20:14:13 -04:00
walkers Changes: 2012-10-03 16:02:42 -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 Proper error handling in NanoScheduler 2012-09-19 17:03:13 -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