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usage convert
Eric Coissac edited this page 2026-09-12 14:00:23 +02:00
Table of Contents

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.

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats