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docs: add obikmer user guide and MkDocs build configuration

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Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
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Eric Coissac
2026-08-13 17:19:01 +02:00
parent 0c86ea0385
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UserDocMD/usage/merge.md
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# 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.