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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/annotate.md
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# 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 |