depristo
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dd978dd525
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misc. changes to python scripts
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3751 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-09 00:13:35 +00:00 |
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depristo
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cf910d9cc2
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misc. useful updates to python library
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3683 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-30 16:33:32 +00:00 |
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depristo
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f5b00c20d0
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Updated python files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 14:15:39 +00:00 |
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depristo
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5289230eb8
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Version 0.2.1 (released) of the TableRecalibrator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 22:50:55 +00:00 |
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depristo
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fb7ba47fff
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Now does really neightbor distance calculation, as well as true snp cluster counting
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@998 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-12 16:29:26 +00:00 |
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depristo
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7fa84ea157
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10x speedup of recalibration walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@954 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-09 15:39:40 +00:00 |
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depristo
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819862e04e
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-05 23:34:37 +00:00 |
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depristo
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3998085e4b
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more and better python scripts for dealing with calls
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@881 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-02 20:37:19 +00:00 |
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depristo
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6adef28b97
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Now supports automatic merging by population
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@864 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-31 15:28:44 +00:00 |
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depristo
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e0803eabd9
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enabled underlying filtering of zero mapping quality reads, vastly improves system performance
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@853 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-29 14:51:08 +00:00 |
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depristo
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8e9e2f4502
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Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 21:06:28 +00:00 |