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cmdLine
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Integrate more feedback on command-line argument system. Focus on help
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2009-05-20 19:01:25 +00:00 |
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duplicates
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Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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2009-05-14 21:06:28 +00:00 |
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fasta
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Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.
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2009-06-01 15:34:38 +00:00 |
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glf
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added some more documentation to the GLF writer and it's supporting classes, and some other fixes
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2009-06-02 14:53:58 +00:00 |
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io
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Lazy creation of output streams. Only create output streams when absolutely necessary.
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2009-05-26 21:56:57 +00:00 |
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sam
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Adding some functions I keep reinventing, especially for testing purposes.
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2009-05-21 19:30:44 +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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windowmaker
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template for windowmaker utility -- total non-functional
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2009-05-07 18:13:03 +00:00 |
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BaseUtils.java
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Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
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2009-05-22 19:32:20 +00:00 |
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BasicPileup.java
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Better accessors for dealing with second base prob pileups
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2009-05-21 22:25:16 +00:00 |
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ComparableSAMRecord.java
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We need to sort cleaned reads ourselves (instead of letting SAMFileWriter
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2009-05-11 15:43:42 +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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Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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2009-05-28 20:13:01 +00:00 |
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GenomeLocSortedSet.java
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Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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2009-05-26 20:57:46 +00:00 |
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GenotypeUtils.java
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minor changes
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2009-05-26 21:03:06 +00:00 |
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JVMUtils.java
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intercept NullPointerException and rethrow it with (marginally) comprehensible error message when an attempt to get class source code location fails
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2009-05-29 15:56:55 +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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Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.
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2009-05-21 19:31:54 +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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Better accessors for dealing with second base prob pileups
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2009-05-21 22:25:16 +00:00 |
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ReadBackedPileup.java
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Better accessors for dealing with second base prob pileups
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2009-05-21 22:25:16 +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 reallocate(int[] orig_array, int new_size) and int[] indexOfAll(String s, int ch); the former is self-explanatory, while the latter returns array of indices of all occurences of ch in the specified string
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2009-05-29 20:15:00 +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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