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 |
asivache
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e95f427965
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Added isReference() to AllelicVariant and updated rodDbSNP accordingly
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@311 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-07 14:49:20 +00:00 |
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asivache
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551ce9130f
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added isBiallelic() to the AllelicVariant interface and to rodDbSNP implementation. We probably don't really know how to deal with non-biallelic sites just as yet...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@294 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-04 21:31:16 +00:00 |
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depristo
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edc44807af
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rod's now have names. Use getName() to access it. Next step is better interface to accessing rods
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 16:41:33 +00:00 |
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asivache
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4bc035d919
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half-way through making rodDbSNP implement AllelicVariant interface; does not work yet
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@267 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 20:48:59 +00:00 |
hanna
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63cd1fe201
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Push core / playground lower into the tree.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-23 23:19:54 +00:00 |