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annotator
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deleting/archiving as instructed
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2010-07-12 16:59:45 +00:00 |
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varianteval
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Fixed memory leak in VariantEval
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2010-07-21 12:35:46 +00:00 |
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AlignedReadsHistoWalker.java
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Genotyper now is using bytes not chars. Passes all tests.
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2010-05-20 21:02:44 +00:00 |
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AlleleBalanceHistogramWalker.java
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Removing more references to VCFRecord
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2010-07-14 11:54:23 +00:00 |
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AnnotationByAlleleFrequencyWalker.java
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Refactoring of the annotation system:
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2010-06-09 17:05:51 +00:00 |
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BaseTransitionTableCalculatorJavaWalker.java
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Genotyper now is using bytes not chars. Passes all tests.
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2010-05-20 21:02:44 +00:00 |
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CreateTiTvTrack.java
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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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DSBWalkerV3.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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DbSNPWindowCounter.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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DesignFileGeneratorWalker.java
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Two fixes together:
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2010-06-24 22:17:03 +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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Can now threshold results based on minimum base and/or mapping quality.
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2010-05-10 19:58:07 +00:00 |
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GCCalculatorWalker.java
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Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets)
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2010-05-19 18:49:51 +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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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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IndelDBRateWalker.java
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No more manually converting VariantContexts to VCFRecords. You should be utilizing VCs and not VCFRecords.
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2010-07-14 05:21:28 +00:00 |
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IndelErrorRateWalker.java
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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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MendelianViolationClassifier.java
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1) When quals/GQs are really integers (x.00), strip off the floating points.
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2010-07-20 18:01:45 +00:00 |
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MismatchCounterWalker.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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MismatchHistoWalker.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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NeighborhoodQualityWalker.java
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Yet more walkers moved to oneoffprojects.
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2009-12-01 21:29:12 +00:00 |
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PairedQualityScoreCountsWalker.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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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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Read error rate is now parallelizable
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2010-05-27 19:00:09 +00:00 |
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ReadQualityScoreWalker.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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ReplaceQuals.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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TestReadFishingWalker.java
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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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TestVariantContextWalker.java
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The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly.
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2010-07-14 04:56:58 +00:00 |
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VCF4ReaderTestWalker.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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VCF4WriterTestWalker.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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ValidateRODForReads.java
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fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!
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2010-06-29 21:38:55 +00:00 |
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