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datasources
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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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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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Use the new downsampling implementation by default
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2012-12-10 09:44:50 -05:00 |
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refdata
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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report
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Added functionality of outputting sorted GATKReport Tables
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2012-12-20 14:02:21 -05:00 |
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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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Active Region extensions must stay on contig
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2013-01-02 14:46:24 -05:00 |
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walkers
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QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass.
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2013-01-02 14:41:29 -05:00 |
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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 |
dcb7735d3c