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cmdLine
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Tweak the arguments passed to the command-line arguments parser so that it fails less often for invalid arguments.
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2009-04-29 14:36:27 +00:00 |
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fasta
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Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.
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2009-04-24 19:40:21 +00:00 |
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threading
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Break out some of the weird inner classes out of the HierachicalMicroScheduler.
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2009-04-29 21:07:07 +00:00 |
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BaseUtils.java
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Privatized constructor to prevent instantiation.
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2009-04-23 17:45:39 +00:00 |
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BasicPileup.java
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Now only distributes 80% of the residual probability to the secondary base, 10% each to the other two bases. Nicer labelling for stringified probability distribution output.
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2009-04-24 03:34:43 +00:00 |
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FileProgressTracker.java
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moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.
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2009-03-27 14:02:55 +00:00 |
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GenomeLoc.java
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Oops, contig index is a zero not one based value
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2009-04-23 19:08:16 +00:00 |
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JVMUtils.java
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Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.
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2009-03-30 23:20:55 +00:00 |
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LogisticRegressor.java
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Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.
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2009-04-28 00:37:48 +00:00 |
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MathUtils.java
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Added multinomialProbability method.
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2009-04-27 15:03:50 +00:00 |
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Pair.java
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Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.
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2009-04-28 00:37:48 +00:00 |
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PathUtils.java
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Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.
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2009-03-30 23:20:55 +00:00 |
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Pileup.java
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General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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2009-04-14 22:13:10 +00:00 |
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Predicate.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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PrimitivePair.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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QualityUtils.java
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Added some stuff for retreiving the base index and probability of a compressed base.
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2009-04-08 15:52:58 +00:00 |
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ReadBackedPileup.java
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Added some methods to retreive the probability distributions of individual bases.
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2009-04-21 22:26:25 +00:00 |
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RefHanger.java
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moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.
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2009-03-27 14:02:55 +00:00 |
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StingException.java
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Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.
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2009-04-16 22:17:25 +00:00 |
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Utils.java
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added k-best quality path enumeration.
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2009-04-22 20:26:51 +00:00 |
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xReadLines.java
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Documentation and cleanup of xReadLines.
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2009-03-25 15:36:21 +00:00 |
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