# annotate

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

```bash
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 |