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datasources
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ExperimentalReadShardBalancerUnitTest was being skipped; fixed
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2012-09-22 01:56:39 -04:00 |
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downsampling
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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)"
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2012-09-10 15:52:39 -04:00 |
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executive
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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filters
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Updated and more thorough version of the BadCigar read filter
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2012-08-17 17:05:27 -04:00 |
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iterators
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Experimental, downsampler-friendly read shard balancer
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2012-09-21 22:17:58 -04:00 |
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refdata
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Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers
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2012-08-30 10:15:10 -04:00 |
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report
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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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samples
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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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traversals
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Refactor TraversalEngine to extract the progress meter functions
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2012-09-10 20:14:13 -04:00 |
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walkers
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In order to be considered an informative read in the PerReadAlleleLikelihoodMap it has to be informative compared to all other alleles not just the worst allele. Also, fixing a bug when there is only one allele in the map.
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2012-10-18 14:31:15 -04:00 |
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CommandLineGATKUnitTest.java
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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.
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2012-07-18 21:48:58 -04:00 |
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EngineFeaturesIntegrationTest.java
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Proper error handling in NanoScheduler
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2012-09-19 17:03:13 -04:00 |
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GenomeAnalysisEngineUnitTest.java
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Removed the "Walker" suffix from all walkers that had it.
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2012-07-20 17:27:11 -04:00 |
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WalkerManagerUnitTest.java
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Fixing walker unit test with the new naming convention
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2012-07-20 17:50:29 -04:00 |
b4e69239dd