Eric Coissac
6acafa7f2c
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.
19 lines
870 B
Markdown
19 lines
870 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 `reindex --approx` ($FP = 1 / 2^{b \cdot z}$). 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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