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bed
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Refactoring intervals, separating the process of parsing interval lists,
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2010-04-13 15:50:38 +00:00 |
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classloader
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fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections
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2010-04-27 17:46:46 +00:00 |
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collections
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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duplicates
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BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
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2010-05-20 14:05:13 +00:00 |
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fasta
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
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fastq
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Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity.
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2009-09-03 17:20:16 +00:00 |
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file
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adding a command line option, -etd (enable threaded debugging), that uses a custom thread pool class to catch exceptions thrown inside of a thread.
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2010-05-27 21:57:56 +00:00 |
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genotype
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Fixed UG parallelization bug. Better integration test to catch this in the future.
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2010-05-25 21:03:45 +00:00 |
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help
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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interval
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Repair code that sorts and merges intervals.
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2010-05-06 22:37:25 +00:00 |
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pileup
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Genotyper now is using bytes not chars. Passes all tests.
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2010-05-20 21:02:44 +00:00 |
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sam
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Optimization of reference window calculation to us bytes not char and no uppercasing since reference and read bases are always uppercase now. Should remove some ~5% of runtime of UG.
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2010-05-26 14:10:26 +00:00 |
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text
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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threading
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
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BaseUtils.java
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Genotyper now is using bytes not chars. Passes all tests.
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2010-05-20 21:02:44 +00:00 |
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GenomeLoc.java
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code cleanup and containsStartPosition function
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2009-10-27 21:53:40 +00:00 |
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GenomeLocParser.java
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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GenomeLocSortedSet.java
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add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal.
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2010-04-15 16:31:43 +00:00 |
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HeapSizeMonitor.java
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Checking in downsampling iterator alongside LocusIteratorByState, and removing
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2010-05-17 21:00:44 +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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Misc. additions to correct utilities
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2010-05-07 21:34:18 +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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QualityUtils.java
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BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
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2010-05-20 14:05:13 +00:00 |
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ReservoirDownsampler.java
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Experimental versions of downsampler and Ryan's deduper are now available either
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2010-05-19 05:40:05 +00:00 |
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SWPairwiseAlignment.java
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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SampleUtils.java
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a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again.
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2010-05-07 03:31:43 +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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Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.
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2010-05-26 22:12:25 +00:00 |
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WilcoxonRankSum.java
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
cded9ec985