docs: add obikmer user guide and MkDocs build configuration

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.
2026-08-13 17:19:01 +02:00
parent 0c86ea0385
commit 6acafa7f2c
28 changed files with 1497 additions and 1 deletions
@@ -0,0 +1,18 @@
+# estimate
+
+Estimate approximate-index parameters (z, evidence bits, false-positive rate) before building an index with `--approx`, without touching any files.
+
+```bash
+obikmer estimate [OPTIONS]
+```
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `-k, --kmer-size` | `31` | Kmer size used at query time (matches `index`'s `--kmer-size`) |
+| `-z, --findere-z` | none | Findere z parameter |
+| `--evidence-bits` | none | Fingerprint bits per slot (b) |
+| `--fp` | none | Target false-positive rate per z-window |
+
+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.