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annotator
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A brief implementation of a QD calculation that is not quite so bimodal for known variants (multiplicatively penalizes QD by (n variant samples)/(n variant alleles) ). Not sure how helpful this will be (which is why it is in oneoffs). Seems nice on MCKD1, but I'm still playing with the optimization.
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2010-08-13 15:42:37 +00:00 |
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varianteval
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Occasionally if a JEXL expression results in no variants being captured (like "QD > 20.0" on filtered variants) the per-sample mapping from samples to eval objects can be empty. This semi-hacky fix prevents null pointer exceptions in setting up the resulting empty table (by jumping straight to it in this case)
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2010-08-13 15:37:45 +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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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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AnnotationByAlleleFrequencyWalker.java
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VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
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2010-08-05 18:47:53 +00:00 |
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BaseTransitionTableCalculatorJavaWalker.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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BeagleOutputByDepthWalker.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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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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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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DSBWalkerV3.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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DbSNPWindowCounter.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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DesignFileGeneratorWalker.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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DownsamplingValidationWalker.java
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A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads,
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2010-05-23 21:49:54 +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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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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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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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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IndelConsistencyReadCounter.java
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Useful tool for calculating the perentage of misaligned reads at homozygous non-ref indel sites
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2010-08-11 17:57:44 +00:00 |
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IndelDBRateWalker.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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IndelErrorRateWalker.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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MendelianViolationClassifier.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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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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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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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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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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RealignedReadCounter.java
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VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
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2010-08-05 18:47:53 +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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TestReadFishingWalker.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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TestVariantContextWalker.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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VCF4WriterTestWalker.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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ValidateRODForReads.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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