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# annotate

Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.

    obikmer annotate INDEX --csv FILE [OPTIONS]
    obikmer annotate INDEX --dump

## Arguments

Argument | Description
--- | ---
`INDEX` | Index directory to annotate (modified in place)

## Options

Option | Default | Description
--- | --- | ---
`--csv` | — | CSV file of metadata to apply (must contain an id column); required unless `--dump` is used
`--sep` | `,` | CSV field separator
`--id-col` | `id` | Name of the column containing genome labels
`--na-value` | `NA` | Value meaning "remove this field" (deletes the existing key if present)
`--no-overwrite` | off | Do not overwrite existing metadata keys
`--dump` | off | Print all genome metadata as CSV to stdout instead of applying a file