depristo
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c66861746a
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improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2819 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-10 16:12:29 +00:00 |
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depristo
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c6d86da4b8
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almost managed to move things around perfectly in move go
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-05 14:18:26 +00:00 |
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depristo
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1d86dd7fd1
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Interface changes following Matt's advice. VariantContexts are now immutable, and there are special mutable versions, in case you need to change things. AttributedObject now a InferredGeneticContext and package protected. VariantContexts are now named, which makes them easier to use with the rod system
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2780 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-04 20:55:49 +00:00 |
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depristo
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d9671dffba
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Documentation for VariantContext. Please read it and start using it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2756 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-01 17:49:51 +00:00 |
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depristo
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956b570c8e
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V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2721 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-28 18:37:17 +00:00 |
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depristo
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f6bca7873c
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V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-28 04:10:16 +00:00 |
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depristo
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3399ad9691
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Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
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2010-01-27 17:19:37 +00:00 |