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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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Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine
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2012-10-22 16:55:06 -04:00 |
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walkers
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Better documentation for ValidateVariants so that people realize it's used for strict validation of the VCF file. Added an option to turn off strict validation and an integration test to cover it.
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2012-10-29 21:47:09 -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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MaxRuntimeIntegrationTest.java
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Add GATK-wide command line argument to control the maximum runtime allowed for the GATK
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2012-10-26 13:18:34 -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 |
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