arq5x/gemini — pull request #48 by chapmanb (2012-10-17 00:13:56+00:00)
Title: Generalize addition of custom annotation columns

Aaron;
These commits generalize the addition of custom annotations:

- Refactors the code to retrieve hits from Tabix indexed files so they handle multiple input types. This keeps all the logic for contig name conversion in a single place.
- Allows custom annotation input files to have GRCh37 coordinates, and cleanly handles searching for contigs not found in the annotation file.
- Refactors the custom annotation code to use one function for committing to the database instead of spreading it out over multiple column types.
- Separates selection and update of sqlite3 tables. On NFS mounted systems, sqlite3 will complain about trying to iterate over a table and update it at the same time.

Hopefully this will make things more robust to annotation file inputs and be easier to maintain over time. Thanks much,
Brad