depristo
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b39b5edca8
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Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-12 19:23:12 +00:00 |
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depristo
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4f4555c80f
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PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-10 22:28:31 +00:00 |
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depristo
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486bef9318
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Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-10 16:25:16 +00:00 |
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depristo
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ee913eca07
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Forgot to check in fix this morning
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2943 348d0f76-0448-11de-a6fe-93d51630548a
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2010-03-05 21:07:19 +00:00 |
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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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5f74fffa02
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Massive improvements to VE2 infrastructure. Now supports VCF writing of interesting sites; multiple comp and eval tracks. Eric will be taking it over and expanding functionality over the next few weeks until it's ready to replace VE1
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2832 348d0f76-0448-11de-a6fe-93d51630548a
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2010-02-12 15:26:52 +00:00 |
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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 |