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.
1.7 KiB
1.7 KiB
convert
Convert an existing index's evidence representation in place, between exact, approximate, and hybrid.
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 for the exact/approximate trade-off and the underlying false-positive model, and estimate to explore parameters beforehand. The index directory is locked for exclusive access during conversion.