# merge

Merge multiple built indexes into a single index.

```bash
obikmer merge -o OUTPUT SOURCE... [OPTIONS]
```

## Arguments

| Argument | Description |
|---|---|
| `SOURCE...` | Index directories to merge (at least one required) |

## Options

| Option | Default | Description |
|---|---|---|
| `-o, --output` | — (required) | Output index directory |
| `--force` | off | Overwrite an existing output directory |
| `--force-presence` | off | Store the merged index as presence/absence even if all sources have counts |
| `--rename-duplicates` | off | Disambiguate duplicate genome labels (`.1`, `.2`, …) instead of failing |
| `--budget-fraction` | `0.5` | Fraction of available RAM reserved as the memory budget for parallel partition merging |

## Behaviour

The output mode is chosen automatically: if every source index stores counts, the merged index stores counts too; otherwise it is presence/absence. `--force-presence` forces presence/absence regardless of the sources.

By default, merging two indexes that share a genome label fails with an error; `--rename-duplicates` instead appends a numeric suffix to keep both copies.