Basic 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].

--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.

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

Provide a path to the output.

--error (unsigned 8 bit integer)

The number of errors Default: 0. Value must be a positive integer or 0.

--tau (double)

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

--threshold (double)

If set, this threshold is used instead of the probabilistic models. Default: nan. Value must be in range [0,1].

--p_max (double)

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

--fpr (double)

The false positive rate used for building the index. Default: 0.05. Value must be in range [0,1].

--pattern (raptor::pattern_size)

The pattern size. Default: Median of sequence lengths in query file.

--threads (unsigned 8 bit integer)

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

--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 pattern, window, kmer/shape, errors, and tau. correction_*.bin: Depends on pattern, window, kmer/shape, p_max, and fpr.