Create a command line tool for helping populate SQL field types for annotation files

compbio-UofT / medsavant

MedSavant is a search engine for genetic variants

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Create a command line tool for helping populate SQL field types for annotation files #61

Closed mfiume closed 10 years ago

mfiume commented 11 years ago

Takes in a tabix file and a XML file with column names and generates a new XML file with field types populated.

Should also output a new Tabix file, with chr, start, end, ref, alt as first 5 columns (NB last two are optional) then the fields described in the input XML file.

jvlasblom commented 11 years ago

This was finished and committed a short time ago, needs testing.

jvlasblom commented 10 years ago

A few annovar annotations have now been tested, suggesting that this feature is indeed working. Closing this issue.