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datasources
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Adding support of X and = CIGAR operators to the GATK
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2012-08-10 14:54:07 -04:00 |
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downsampling
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Make downsampler classes themselves generic (instead of just the Downsampler interface)
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2012-06-13 16:43:39 -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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Fix for Adam K's reported bug: we weren't handling reads that were entirely insertions properly in LIBS. Specifically, the event bases were off-by-one (which was disasterous in Adam's case with a 1bp read). Added a unit test to cover this case.
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2012-08-20 23:12:41 -04:00 |
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refdata
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RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions
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2012-07-25 22:05:04 -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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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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walkers
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CombineVariants outputs the first non-MISSING qual, not the maximum
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2012-08-19 10:29:38 -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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Sorting out HMS error handling (fingers crossed)
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2012-07-25 23:13:12 -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 |
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