query

Query an index with sequences and annotate each query with the kmer matches found.

obikmer query INDEX INPUTS... [OPTIONS]

Arguments

Argument	Description
`INDEX`	Index directory to query against
`INPUTS...`	Input sequence files (FASTA/FASTQ, gzip optional); at least one required

Option	Default	Description
`--detail`	off	Report per-position, per-genome coverage vectors in the output
`--count-missing`	off	Also count query kmers absent from the index
`--force-presence`	off	Report presence (0/1) per genome instead of raw counts
`--presence-threshold`	`1`	Minimum accumulated count to declare a genome present (implies `--force-presence`)
`-z, --findere-z`	derived from the index metadata	Override the Findere z parameter
`-T, --threads`	detected core count	Number of worker threads
`--chunk-size`	auto-sized (available RAM ÷ threads, clamped to 4–256 MiB)	I/O chunk size, in MiB
`--max-open-files`	`threads / 4` (min 1)	Maximum number of input files open simultaneously

FASTA on stdout, one record per query, annotated in the OBITools-style header format >id {"key":value,...}:

kmer_count: total number of kmers matched
kmer_missing: number of query kmers absent from the index (only with --count-missing)
kmer_strict_matches: per-genome match counts
coverage: per-position, per-genome coverage vectors (only with --detail)

--mismatch is accepted by the CLI but not currently functional; using it produces a warning and is ignored.