NAME

       needle-count - Get expression value depending on minimizers. This function is only used to
       test the validity of Needle's estimation approach. It estimates the expression  value  for
       all  sequences  in  the  genome file based on the exact minimiser occurrences of the given
       sequence files.

POSITIONAL ARGUMENTS

       ARGUMENT-1 (List of std::filesystem::path)
              Please provide at least one sequence file. Default: [].

OPTIONS

   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].

       -k, --kmer (unsigned 8 bit integer)
              Define k-mer size for the minimisers. Default: 20. Default: 20.

       -w, --window (unsigned 32 bit integer)
              Define window size for the minimisers. Default: 60. Default: 0.

       --shape (unsigned 64 bit integer)
              Define a shape for the minimisers by the decimal of a bitvector, where 0 symbolizes
              a position to be ignored, 1 a position considered. Default: ungapped. Default: 0.

       --seed (unsigned 64 bit integer)
              Define seed for the minimisers. Default: 0.

       -o, --out (std::filesystem::path)
              Directory, where output files should be saved. Default: "./".

       -t, --threads (unsigned 8 bit integer)
              Number of threads to use. Default: 1. Default: 1.

       -g, --genome (std::filesystem::path)
              Please provide one sequence file with transcripts. Default: "".

       --exclude (std::filesystem::path)
              Please provide one sequence file with minimizers to ignore. Default: "".

       -p, --paired
              If set, experiments are paired. Default: Not paired.

VERSION

       Last update:
       needle-count version:
       SeqAn version: 3.2.0