obikmer/UserDocMD/usage/query.md

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

Options

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

Output

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.