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compbio-UofT / medsavant

MedSavant is a search engine for genetic variants
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Cut out wasted annotation steps #260

Closed mfiume closed 10 years ago

mfiume commented 10 years ago

I'm fairly sure that when I import a file into an existing database, and don't change any configuration of the database (e.g. change the annotations), we reannotate everything from scratch. screen shot 2014-01-22 at 12 07 30 am

This is a huge waste and will cripple us for large projects. If this is true, we need to create a patch that checks if the annotations and custom fields are the same for this upload as they are for the latest variant table and skips the relevant parts.

jvlasblom commented 10 years ago

It should not be necessary to check if annotations and custom fields are the same for the upload and the existing variant table. It must be the case that loading a new VCF will use the same annotations as the table. (ImportUpdateManager.doImport does not accept new annotations)

jvlasblom commented 10 years ago

No wasted steps during VCF removal, closing.