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.
879 B
879 B
estimate
Estimate approximate-index parameters (z, evidence bits, false-positive rate) before building an index with --approx, without touching any files.
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 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.