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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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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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classloader
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Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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2010-11-12 20:14:28 +00:00 |
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collections
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renaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
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2010-10-08 14:08:28 +00:00 |
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duplicates
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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exceptions
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Queue UI Improvements:
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2010-10-26 19:49:08 +00:00 |
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fasta
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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fastq
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Moving StingException
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2010-09-12 14:34:15 +00:00 |
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file
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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genotype
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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help
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Excluding the QFunction log files from the set of files to delete on completion.
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2010-11-18 20:22:01 +00:00 |
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instrumentation
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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interval
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Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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2010-11-12 20:14:28 +00:00 |
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pileup
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Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.
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2010-11-19 19:59:05 +00:00 |
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report
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Recent changes to the build system make the build system complain loudly about
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2010-09-24 22:09:12 +00:00 |
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sam
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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text
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GenotypeConcordance now prints interesting sites more nicely. RMDTrackBuilder is now uses the root class FeatureSource not BasicFeatureSource.
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2010-10-20 00:29:02 +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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vcf
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Bug fix for variants in VCF header fetching to avoid null pointer when a VariantContext tribble codec doesn't have a header
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2010-11-05 12:43:25 +00:00 |
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wiggle
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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yaml
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Updated from SnakeYAML 1.6 to 1.7.
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2010-09-22 19:47:49 +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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CardinalityCounter.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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DisjointSet.java
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Moved phasing classes out of playground! The code is still under production, though...
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2010-09-28 23:21:28 +00:00 |
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DoublyLinkedList.java
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Moved phasing classes out of playground! The code is still under production, though...
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2010-09-28 23:21:28 +00:00 |
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GenomeLoc.java
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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GenomeLocParser.java
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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GenomeLocSortedSet.java
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Convert GenomeLocParser into an instance variable. This change is required
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2010-11-10 17:59:50 +00:00 |
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Graph.java
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Moved phasing classes out of playground! The code is still under production, though...
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2010-09-28 23:21:28 +00:00 |
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GraphEdge.java
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Moved phasing classes out of playground! The code is still under production, though...
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2010-09-28 23:21:28 +00:00 |
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HeapSizeMonitor.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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MalformedGenomeLocException.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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MathUtils.java
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VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary
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2010-11-15 22:19:22 +00:00 |
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PathUtils.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +00:00 |
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PreciseNonNegativeDouble.java
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Minor JAVA visibility updates
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2010-11-16 15:28:58 +00:00 |
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QualityUtils.java
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Checking in everyone's changes to the variant recalibrator. We now calculate the variant quality score as a LOD score between the true and false hypothesis. Allele Count prior is changed to be (1 - 0.5^ac). Known prior breaks out HapMap sites
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2010-08-05 14:12:19 +00:00 |
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ReservoirDownsampler.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +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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More changes to Variant Eval and Genotype Concordance (passes all integration tests):
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2010-10-15 12:40:36 +00:00 |
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SequenceDictionaryUtils.java
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- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
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2010-11-15 20:34:04 +00:00 |
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Utils.java
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Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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2010-11-12 20:14:28 +00:00 |
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WilcoxonRankSum.java
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Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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2010-09-12 15:07:38 +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 |
374c0deba2