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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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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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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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genotype
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adding VC adaptor for GELI, along with unit tests.
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2010-04-23 05:28:39 +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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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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pileup
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Always return deleted bases in upper case
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2010-04-20 19:17:40 +00:00 |
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sam
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Pulling out the left-alignment code for indels so that other walkers can use it.
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2010-04-23 16:12:34 +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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Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful.
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2010-03-28 21:45:22 +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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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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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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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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Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution.
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2010-03-17 20:41:42 +00:00 |
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ReservoirDownsampler.java
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Rev the reservoir downsampler to support partitioning through a functor.
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2010-04-21 19:50:26 +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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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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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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Optimized the join(..) method.
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2010-04-30 15:55:07 +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 |
8b2ce128b5