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arguments
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Better handling of enums by the command-line argument system.
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2010-01-20 21:36:46 +00:00 |
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contexts
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PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample
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2010-03-10 22:28:31 +00:00 |
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datasources
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some rods-for-reads cleaning and performance improvements.
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2010-03-10 22:54:58 +00:00 |
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examples
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Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes
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2010-02-05 21:47:54 +00:00 |
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executive
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Partially reclaim performance lost during integration test fixes.
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2010-03-09 12:36:11 +00:00 |
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filters
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Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark.
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2010-01-03 21:31:04 +00:00 |
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io
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Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.
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2010-03-09 03:41:07 +00:00 |
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iterators
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In the new sharding system, if no read group is present, hallucinate one. Added
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2010-03-07 23:01:34 +00:00 |
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refdata
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Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext.
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2010-03-10 16:25:16 +00:00 |
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traversals
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Fix bug that's been in the GATK for a very long time: update nReads (as well
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2010-03-08 22:44:54 +00:00 |
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walkers
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Fixed strand bias calculation because of -Infinity issues.
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2010-03-11 16:05:51 +00:00 |
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CommandLineExecutable.java
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Looks bigger than it is:
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2010-01-15 00:14:35 +00:00 |
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CommandLineGATK.java
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Update our error messages to point to getsatisfaction.com/gsa.
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2010-01-27 19:16:28 +00:00 |
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GenomeAnalysisEngine.java
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some rods-for-reads cleaning and performance improvements.
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2010-03-10 22:54:58 +00:00 |
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Reads.java
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changes to intelligently log overflowing locus pile-ups.
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2010-01-20 08:09:48 +00:00 |
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WalkerManager.java
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Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built.
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2010-01-20 19:18:19 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
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