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Update documentation for CLI command renames and new commands

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Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
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Eric Coissac
2026-08-28 23:06:05 +02:00
parent 95fa0c93b2
commit caf59b5658
38 changed files with 666 additions and 2433 deletions
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UserDocMD/usage/convert.md
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# convert
Convert an existing index's evidence representation in place, between exact, approximate, and hybrid.
```bash
obikmer convert INDEX (--exact-evidence | --approx-evidence BITS | --hybrid-evidence) [OPTIONS]
```
## Arguments
| Argument | Description |
|---|---|
| `INDEX` | Index directory to convert (modified in place) |
## Options
Exactly one of the first three is required:
| Option | Description |
|---|---|
| `--exact-evidence` | Convert to exact evidence (zero false positives) |
| `--approx-evidence BITS` | Convert to approximate (fingerprint-only) evidence; `BITS` = fingerprint bits per slot (b) |
| `--hybrid-evidence` | Convert to hybrid evidence (both exact and approximate bundles kept) |
| `--evidence-bits BITS` | Fingerprint bits per slot (b) — required with `--hybrid-evidence` when the source index is currently exact; rejected otherwise (the source already fixes `b`) |
| `-z, --findere-z Z` | Findere z parameter: number of consecutive stored kmers that must all match to confirm a hit. This does not shorten the indexed kmer length (fixed forever at `index` build time) — it extends the effective match window: on a k=31 index, `z=2` requires 32 consecutive matching bases, not 30 |
| `--fp FP` | Target false-positive rate per z-window (e.g. `0.01`); derives `b` or `z` when one of them isn't given directly |
| `--block-size N` | Block size for exact evidence's on-disk index (unitigs per block). Ignored when converting to pure approximate evidence. Default `1` |
See [`index`](index_command.md#exact-vs-approximate-evidence) for the exact/approximate trade-off and the underlying false-positive model, and [`estimate`](estimate.md) to explore parameters beforehand. The index directory is locked for exclusive access during conversion.