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How to handle duplicate IDs

See original GitHub issue

Currently db creation uses INSERT OR IGNORE rather than just INSERT. The side effect is that only the first instance of a unique ID is entered into the database and all other instances with the same ID are ignored.

Should duplicate IDs in a GFF file be considered an error?

Issue Analytics

State:
Created 11 years ago
Comments:8 (8 by maintainers)

Top GitHub Comments

1reaction

dalercommented, Feb 28, 2013

True, and since the exons and CDSs in GTFs don’t usually have unique IDs, there’s already a mechanism for creating them on the fly. So to the user it may be as simple as providing create_db() a merge_strategy= kwarg, say one of 'merge' (acts like we’ve been talking about above), 'create_unique' (makes a new ID upon collision), or 'error' (raises NonUniqueIDError or something).

0reactions

dalercommented, Jan 16, 2015

closing since this has been implemented for a while

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