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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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Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.
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2010-09-12 14:02:43 +00:00 |
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classloader
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Fix newly-introduced bug in the PluginManager/DynamicClassResolutionException
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2010-09-30 19:07:05 +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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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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exceptions
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Better message
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2010-10-10 20:11:51 +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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Naughty use of Strings in HaplotypeScore literally double the runtime of Unified Genotyper. Moved over to bytes and no longer allow Strings in the Haplotype util class. New round of profiling on tap for tomorrow.
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2010-10-20 03:32:21 +00:00 |
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help
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A mechanism for supplying attribution text -- mainly useful for external
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2010-10-01 18:31:19 +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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bug fix
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2010-10-15 16:27:40 +00:00 |
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pileup
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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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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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Reverting Matt's change from yesterday which I accidentally blew away when trying to cope with the stupid svn update issues we've been plagued with recently.
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2010-10-14 14:40:42 +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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Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are:
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2010-09-28 02:16:25 +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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Added startsBefore, startsAfter, and minDistance [calculates distance between any pair of bases in the two GenomeLocs]
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2010-10-20 19:12:34 +00:00 |
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GenomeLocParser.java
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Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.
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2010-09-25 02:49:30 +00:00 |
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GenomeLocSortedSet.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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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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QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG
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2010-09-03 18:21:43 +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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Updated to work exclusively in log10 space
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2010-08-19 21:31:07 +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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Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.
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2010-09-25 02:49:30 +00:00 |
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Utils.java
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Massive review of maybe 50% of the exceptions in the GATK. GATKException is a tmp. tracker so that I can tell which StingExceptions I've reviewed. Please don't use it. If you are working on new code and are considering throwing exceptions, it's either UserError or StingException, please
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2010-09-09 23:21:17 +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 |
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