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cmdLine
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Bring new command-line argument parsing system live.
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2009-05-06 18:16:11 +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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io
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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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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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Choose a random base to stick in the pileup if the 2nd-best base matches the best base.
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2009-05-01 06:27:37 +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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Only prints about first contig info setting
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2009-04-30 22:14:26 +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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A better (less overflow-y) implementation of multinomialProbability().
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2009-05-01 06:28:16 +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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More ways to access quality utils
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2009-04-30 22:12:07 +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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Added convenience functions for RefHanger
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2009-05-01 21:14:40 +00:00 |
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StingException.java
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Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it.
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2009-04-29 22:09:41 +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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