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annotator
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Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.
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2010-11-03 19:23:03 +00:00 |
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haplotype
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Simple test code from Steve Schaffner to compute R^2 and D'. This is just for educational purposes. Don't use this code for anything, ever!
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2010-08-23 05:06:16 +00:00 |
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phasing
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Updated phasing pipeline to properly read samples from VCF and BAM files
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2011-02-02 07:16:05 +00:00 |
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varianteval
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Fixed import statements.
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2011-01-31 19:26:37 +00:00 |
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vcftools
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renamed genotypesArePhased to isPhased, as the previous name was incorrect for several reasons. Added setPhase() to MutableGenotype. Other classes changed to reflect renaming to isPhased(). CombineVariants now supports an experimental MASTER mode where it consumes -B:master,vcf and -B:xi,vcf for any number i and updates the master with phasing information in xi.
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2010-12-22 17:42:05 +00:00 |
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AlignedReadsHistoWalker.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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AlleleBalanceHistogramWalker.java
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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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AnnotationByAlleleFrequencyWalker.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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AssessLikelihoodsAtTruth.java
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oneoffs walker to assess GLs at truth sites
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2011-01-26 14:59:05 +00:00 |
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AssessMissingBroadCalls.java
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Not supported. I'm checking this in for Ryan only.
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2010-11-30 16:59:18 +00:00 |
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AssessSimulatedPerformance.java
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V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R
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2010-11-08 21:01:33 +00:00 |
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BeagleOutputByDepthWalker.java
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Trivial update for data processing paper: change syntax of output argument for Beagle by depth walker to update to new GATK format.
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2010-11-24 01:45:44 +00:00 |
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CGIndelConverter.java
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My only experience with getting external groups (GAP,dbSNP) to use VCF has been painful at best, so I'm not holding my breath to get indels for CG in VCF. To that extent, here's a oneoffs walker to convert from CG format to VCF for all 'del' & 'ins' types (but not 'sub' types, since they're too complex to code up in VCF and I don't care about them for now). rs ids are included.
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2010-10-26 17:53:14 +00:00 |
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CountIntervals.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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CreateTiTvTrack.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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DSBWalkerV3.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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DbSNPWindowCounter.java
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A significant refactoring of the ROD system, done largely to simplify the process of
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2010-12-31 04:52:22 +00:00 |
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DesignFileGeneratorWalker.java
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java changes:
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2010-12-12 05:10:45 +00:00 |
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DetectWGAWalker.java
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deleting accidentally committed junk
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2010-10-08 15:13:01 +00:00 |
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DownsamplingValidationWalker.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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ErrorRatePerReadPosition.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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GCCalculatorWalker.java
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removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.
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2010-09-15 22:54:49 +00:00 |
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IOCrusherWalker.java
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Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
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2010-05-19 23:27:55 +00:00 |
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IndelAnnotator.java
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Oops...forgot to commit the changes that allow primitive VCF streaming.
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2011-01-12 21:54:51 +00:00 |
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IndelConsistencyReadCounter.java
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Renamed getName() to getSource() in VariantContext to be more accurate
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2010-10-27 02:21:41 +00:00 |
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IndelDBRateWalker.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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IndelErrorRateWalker.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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MarkIntervals.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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MendelianViolationClassifier.java
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Fixed import statements.
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2011-01-31 19:26:37 +00:00 |
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MismatchCounterWalker.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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MismatchHistoWalker.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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NeighborhoodQualityWalker.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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PairedQualityScoreCountsWalker.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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QualityScoreByStrandWalker.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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ReadErrorRateWalker.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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ReadQualityScoreWalker.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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RealignedReadCounter.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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ReplaceQuals.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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SimulateReadsForVariants.java
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V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R
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2010-11-08 21:01:33 +00:00 |
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TestReadFishingWalker.java
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Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.
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2010-12-05 18:29:39 +00:00 |
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TestVariantContextWalker.java
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A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running...
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2010-10-12 18:39:56 +00:00 |
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VCF4WriterTestWalker.java
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A significant refactoring of the ROD system, done largely to simplify the process of
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2010-12-31 04:52:22 +00:00 |
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ValidateRODForReads.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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