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compbio-UofT / medsavant

MedSavant is a search engine for genetic variants
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Update BasicVariantColumns for new columns #273

Open ronammar opened 10 years ago

ronammar commented 10 years ago

Update BasicVariantColumns to include new default columns for 1.2 including: 2 Jannovar columns (EFFECT, HGVS - both extracted from the INFO field), defualt allele frequency columns for 1000g and 6500ex, Clinvar fields (there will likely be 5 - this isn't 100% finished yet).

jvlasblom commented 10 years ago

This is probably not want we want to do. The Jannovar columns aren't always there -- there's a checkbox which makes Jannovar columns optional. Similarly, the user can override the default annotations, so one cannot assume that these are always present either. Also, the indices at which these columns are located are variable.

ronammar commented 10 years ago

Well, then we have to detail what the precise name of each column will be in the DB so that a user can use an indexOf-like method to obtain the columns without prior knowledge of the DB structure (which is essentially what I am doing for these columns right now)

jvlasblom commented 10 years ago

I think the way to get at these columns is going to be different than what you have been doing for basicvariantcolumns, but I can appreciate the need to clarify how to get at the various data associated with each variant.

On 03/02/14 12:28 PM, ronammar wrote:

Well, then we have to detail what the precise name of each column will be in the DB so that I user can use an indexOf-like method to obtain the columns without prior knowledge of the DB structure (which is essentially what I am doing for these columns right now)

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/273#issuecomment-33978155.