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cmdLine
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General-purpose management of output streams.
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2009-08-23 00:56:02 +00:00 |
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containers
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A priority-queue-like container that allows you to add a specified number of elements. When the limit has been reached, new additions replace the lower scoring elements.
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2009-06-24 15:39:47 +00:00 |
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duplicates
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Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
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2009-07-06 15:41:30 +00:00 |
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fasta
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Better handling of fasta files with non-standard extensions.x
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2009-07-09 18:18:48 +00:00 |
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genotype
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vcf changes from Richards comments, fixed a test case
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2009-08-25 14:32:16 +00:00 |
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io
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
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2009-06-17 16:27:48 +00:00 |
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sam
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General-purpose management of output streams.
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2009-08-23 00:56:02 +00:00 |
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threading
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
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2009-06-17 16:27:48 +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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AlignmentUtils.java
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-set indel cleaning walkers to be in core package
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2009-07-24 05:23:29 +00:00 |
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BaseUtils.java
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Added : String reverse(String s) - reverses a string
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2009-08-12 20:16:22 +00:00 |
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BasicPileup.java
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Cleaned division of responsibilities between arguments to map function. Reference has been changed
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2009-08-04 21:01:37 +00:00 |
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ComparableSAMRecord.java
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only compare pair position for paired end reads
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2009-07-08 04:07:08 +00:00 |
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ExpandingArrayList.java
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Updated version of the recalibration tool
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2009-06-19 17:45:47 +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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Windowed access to the reference.
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2009-08-05 16:29:15 +00:00 |
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GenomeLocParser.java
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Made the size zero interval file checker emit a warnUser if we're not in unsafe mode.
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2009-08-21 14:40:57 +00:00 |
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GenomeLocSortedSet.java
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added a big speed-up for interval list input processing. With large interval sets this was taking way too long...
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2009-07-13 22:00:00 +00:00 |
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GenotypeUtils.java
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-Output single filtration stats file with input from all filters
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2009-08-03 20:44:21 +00:00 |
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JVMUtils.java
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Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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2009-07-29 16:11:45 +00:00 |
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ListUtils.java
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Added ability to sample from a list *without* replacement.
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2009-07-23 21:00:19 +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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MalformedGenomeLocException.java
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A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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2009-06-02 18:14:46 +00:00 |
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MathUtils.java
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Added several useful routines to MathUtils for summing and bounds checking of doubles
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2009-08-05 00:41:31 +00:00 |
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PackageUtils.java
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Switched to Reflections (http://code.google.com/p/reflections/) project for
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2009-07-21 18:32:22 +00:00 |
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Pair.java
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The building blocks for segmenting covariate counting data by read group.
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2009-06-04 19:55:24 +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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Version 0.2.1 (released) of the TableRecalibrator
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2009-06-25 22:50:55 +00:00 |
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ReadBackedPileup.java
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Cleaned division of responsibilities between arguments to map function. Reference has been changed
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2009-08-04 21:01:37 +00:00 |
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RefHanger.java
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Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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2009-06-30 19:17:24 +00:00 |
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SWPairwiseAlignment.java
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-set indel cleaning walkers to be in core package
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2009-07-24 05:23:29 +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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General-purpose management of output streams.
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2009-08-23 00:56:02 +00:00 |
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package.html
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
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2009-06-17 16:27:48 +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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