30 lines
1.1 KiB
Markdown
30 lines
1.1 KiB
Markdown
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# merge
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Merge multiple built indexes into a single index.
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```bash
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obikmer merge -o OUTPUT SOURCE... [OPTIONS]
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `SOURCE...` | Index directories to merge (at least one required) |
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## Options
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| Option | Default | Description |
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|---|---|---|
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| `-o, --output` | — (required) | Output index directory |
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| `--force` | off | Overwrite an existing output directory |
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| `--force-presence` | off | Store the merged index as presence/absence even if all sources have counts |
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| `--rename-duplicates` | off | Disambiguate duplicate genome labels (`.1`, `.2`, …) instead of failing |
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| `--budget-fraction` | `0.5` | Fraction of available RAM reserved as the memory budget for parallel partition merging |
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## Behaviour
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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.
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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.
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