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].

-i, --in (std::filesystem::path)

Directory where input files can be found. Default: "./".

-o, --out (std::filesystem::path)

Directory, where output files should be saved. Default: "expressions.out".

-t, --threads (unsigned 8 bit integer)

Number of threads to use. Default: 1. Default: 1.

-m, --normalization-mode

Set, if normalization is wanted. Normalization is achieved bydividing the expression value with the expression threshold of the first ibf. Only make sense if every bin has its own expression thresholds (which is the case if expression thresholds were generated automatically).Default: False.