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# merge

Merge multiple built indexes into a single index.

    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.