ebanks
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0e9a6826b0
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Update to VCF code to get it up to spec.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-03 06:12:42 +00:00 |
depristo
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9a6b384adb
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Support for no qual fields in VCF; better support for Mendelian violation calculations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-26 00:29:17 +00:00 |
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depristo
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8072e9aed5
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should never commit without running intergration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-12 23:42:37 +00:00 |
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depristo
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934d4b93a2
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VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-09 19:02:25 +00:00 |
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depristo
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94f892ad42
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VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-09 01:22:05 +00:00 |
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depristo
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3b1ab86d11
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Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2803 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-06 16:26:06 +00:00 |
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depristo
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1494dc875f
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fixing up tests. Moves are complete
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2789 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-05 14:24:00 +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 |