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analysis
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Initial commit of items for analyzing amino acid transitions in variant eval. Blew up my subversion by coding locally while i did not have internet. I hope this doesn't bust any integrationtests since I changed no existing code but...who knows. Crossing my fingers.
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2010-06-29 20:57:18 +00:00 |
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bed
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making 'parseLocation' public static - as simple as the logic is, it's better kept in one place and I need it!
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2010-06-11 18:19:59 +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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Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too.
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2010-07-19 22:13:18 +00:00 |
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duplicates
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A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.
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2010-06-20 04:42:26 +00:00 |
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fasta
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IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.
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2010-07-01 04:40:31 +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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updating the Tribble track loading code to use the new shared locks, updated lots of new tests, add infrastructure for the TreeInterval, and removed the old locking class.
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2010-07-20 07:08:10 +00:00 |
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genotype
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a) Bug fix in VCFHeader parsing - Info fields were not being parsed properly, with the result that the Count field was not being properly displayed in records (e.g. if Count=0 for a particular field, the INFO tag was still being displayed as ...;Field=x;... instead of ...;Field;...
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2010-07-22 02:36:45 +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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Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.
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2010-06-21 21:49:41 +00:00 |
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pileup
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Cleanup for Steve Hershman's issue. In the midst of doing this, I discovered
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2010-07-16 18:57:58 +00:00 |
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sam
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Added utility shortcut method: getOriginalQualsInCycleOrder(read)
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2010-07-22 15:44:25 +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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wiggle
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Support for generating (very basic) wiggle files for use with IGV (see UCSC for wiggle spec); and a walker to take in a variant track and create a transition transversion rate track for the whole genome (due to the wiggle spec, this has to be done by chromosome). It's interesting to see the effect of genes!
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2010-07-21 18:04:30 +00:00 |
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BaseUtils.java
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Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.
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2010-07-19 19:10:29 +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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Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.
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2010-06-21 21:49:41 +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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Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept
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2010-06-13 01:47:02 +00:00 |
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SWPairwiseAlignment.java
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Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.
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2010-05-27 23:16:00 +00:00 |
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SampleUtils.java
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The first step in integrating Jim's tree based index scheme:
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2010-07-19 04:49:27 +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 |
3308d956f4