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Allows.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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By.java
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Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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2009-05-15 21:02:12 +00:00 |
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CountLociWalker.java
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N-way parallelism. Works for small test cases. Untested for large test cases.
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2009-05-01 19:34:09 +00:00 |
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CountReadsWalker.java
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Changed reads traversals from providing a LocusContext from which the reference sequence
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2009-05-11 22:45:11 +00:00 |
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DataSource.java
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Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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2009-05-15 21:02:12 +00:00 |
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DepthOfCoverageWalker.java
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Switch to better mechanism for supplying a default.
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2009-05-07 01:22:01 +00:00 |
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DuplicateWalker.java
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More improvements to the duplicate quality combiner, making progress towards a clean system
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2009-05-21 22:26:57 +00:00 |
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LocusWalker.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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LocusWindowWalker.java
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add the @Requires for this walker
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2009-05-20 17:03:12 +00:00 |
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NullWalker.java
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Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.
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2009-04-03 19:54:54 +00:00 |
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PileupWalker.java
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qualsAsInt argument for Pileup
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2009-06-04 18:37:39 +00:00 |
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PrintLocusContextWalker.java
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Reintroduce support for interval-based traversals.
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2009-05-18 22:54:18 +00:00 |
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PrintReadsWalker.java
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QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
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2009-05-21 18:30:45 +00:00 |
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RMD.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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ReadWalker.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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RefWalker.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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Requires.java
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@Required / @Allows flags for main arguments.
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2009-05-19 23:26:17 +00:00 |
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TreeReducible.java
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N-way parallelism. Works for small test cases. Untested for large test cases.
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2009-05-01 19:34:09 +00:00 |
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ValidatingPileupWalker.java
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Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.
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2009-05-26 15:58:21 +00:00 |
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Walker.java
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intervals_file + genome_loc => intervals.
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2009-05-12 01:04:18 +00:00 |
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WalkerName.java
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Make command-line arguments available in walker constructor, provide back door from
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2009-03-26 20:45:27 +00:00 |
9de3e58aa8