General options

--index (std::filesystem::path)

Provide a valid path to an index. Parts: Without suffix _0

--query (std::filesystem::path)

Provide a path to the query file. The input file must exist and read permissions must be granted. Valid file extensions are [embl,fasta,fa,fna,ffn,faa,frn,fas,fastq,fq,genbank,gb,gbk,sam], possibly followed by [bz2,gz,bgzf].

--output (std::filesystem::path)

A valid path for the output file. Write permissions must be granted.

--threads (unsigned 8 bit integer)

The number of threads to use. Default: 1. Value must be a positive integer.

--quiet

Do not print time and memory usage.

Threshold method options

If no option is set, --error 0 will be used as default.
Setting --query_length also skips validations associated with the query length, e.g., too long/short queries or a high variance in the query lengths. Notably, queries that are shorter than the window size result in undefined behavior.

--error (unsigned 8 bit integer)

The number of errors. Mutually exclusive with --threshold. Default: 0. Value must be a positive integer or 0.

--threshold (double)

Ratio of k-mers that need to be found for a hit to occur. Mutually exclusive with --error. Default: None. Value must be in range [0,1].

--query_length (unsigned 64 bit integer)

The query length. Only influences the threshold when using --error. Enables skipping of the query length computation for both --error and --threshold. Default: Median of sequence lengths in query file.

Dynamic thresholding options

These option have no effect when using --threshold or k-mer size == window size.
A higher threshold means that less, in the extreme case even false negative, results will be produced.
A lower threshold means that more, possibly false positive, results will be produced.

--tau (double)

The higher tau, the lower the threshold. Default: 0.9999. Value must be in range [0,1].

--p_max (double)

The higher p_max, the lower the threshold. Default: 0.15. Value must be in range [0,1].

--cache-thresholds

Stores the computed thresholds with an unique name next to the index. In the next search call using this option, the stored thresholds are re-used. Two files are stored:

threshold_*.bin: Depends on query_length, window, kmer/shape, errors, and tau.

correction_*.bin: Depends on query_length, window, kmer/shape, p_max, and fpr.

Common options

-h, --help

Prints the help page.

-hh, --advanced-help

Prints the help page including advanced options.

--version

Prints the version information.

--copyright

Prints the copyright/license information.

--export-help (std::string)

Export the help page information. Value must be one of [html, man, ctd, cwl].