Eric Coissac
caf59b5658
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.
19 lines
879 B
Markdown
19 lines
879 B
Markdown
# estimate
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Estimate approximate-index parameters (z, evidence bits, false-positive rate) before building an index with `--approx`, without touching any files.
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```bash
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obikmer estimate [OPTIONS]
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```
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## Options
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| Option | Default | Description |
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| `-k, --kmer-size` | `31` | Kmer size used at query time (matches `index`'s `--kmer-size`) |
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| `-z, --findere-z` | none | Findere z parameter |
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| `--evidence-bits` | none | Fingerprint bits per slot (b) |
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| `--fp` | none | Target false-positive rate per z-window |
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Any two of `-z`, `--evidence-bits`, `--fp` may be given; the third is derived using the same model as `index --approx` and `convert --approx-evidence` ($FP = 1 / 2^{b \cdot z}$). The report printed to stdout includes: query $k$, effective indexed $k$ ($k-z+1$), $z$, evidence bits, per-kmer false-positive rate, and per-z-window false-positive rate.
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