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augur db with import/export of metadata #1094

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augur db with import/export of metadata #1094

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Commits on Jan 11, 2023

  1. io: Define potential strain column names in a new file 

    This avoids re-defining these values at each use case and prevents them
from getting out of sync.
    @victorlin
    victorlin committed Jan 11, 2023
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Commits on Jan 12, 2023

  1. io: Add class interfaces for working with SQLite3 and data files 

    These are in anticipation of usage by the augur db subcommand, but can
be used by other subcommands such as augur filter.
    @victorlin
    victorlin committed Jan 12, 2023
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  2. db: Implement basic import/export of data 

    This adds a basic interface to enable working in a world of SQLite3.

See functional test files for example usage.
    @victorlin
    victorlin committed Jan 12, 2023
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  3. db: Index the ID columns 

    This serves to detect duplicates and speed up strain-based queries.
    @victorlin
    victorlin committed Jan 12, 2023
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  4. db/import: Add argument to skip strain indexing

    @victorlin
    victorlin committed Jan 12, 2023
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  5. io/sqlite3: Add option to use in-memory database 

    This is unused but can be handy.
    @victorlin
    victorlin committed Jan 12, 2023
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