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annotator
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Removing obsolete rod; no longer needed given previous addition to SampleUtils.
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2010-06-16 20:03:14 +00:00 |
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varianteval/multisample
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Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
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2010-05-28 14:52:44 +00:00 |
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vcftools
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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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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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Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
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2010-05-28 14:52:44 +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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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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updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function.
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2010-06-04 06:34:26 +00:00 |
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DesignFileGeneratorWalker.java
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VariantEvalWalker now takes indels if you throw the -dels flag. IndelLengthHistogram appears to be working properly, it is turned off by default (as it is experimental) but you can turn it on in your own repository.
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2010-05-26 20:03:14 +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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VCF moved over to tribble.
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2010-05-05 17:28:48 +00:00 |
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IndelDBRateWalker.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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IndelErrorRateWalker.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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MendelianViolationClassifier.java
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Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity.
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2010-06-09 18:05:37 +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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OppositeHomozygoteClassifier.java
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Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf:
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2010-06-08 03:56:07 +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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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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TestVariantContextWalker.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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VCF4ReaderTestWalker.java
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Optimized, nearly complete VCF4 reader 2-4x faster than the previous implementation, along with a VCF4 reader performance testing walker that can read 3/4 files, useful for benchmarking
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2010-06-04 18:11:38 +00:00 |
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VCFReferenceFixerWalker.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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