Options for clc_mapping_table

usage: clc_mapping_table [options] <cas file>
  Print information about each match in a read mapping. The columns are:
    Read number
    Read name (enable using the `-n' option)
    Read length
    Read position for alignment start
    Read position for alignment end
    Reference sequence number
    Reference position for alignment start
    Reference position for alignment end
    Whether the read is reversed (0 = no, 1 = yes)
    Number of matches
    Whether the read is paired with the next one (0 = no, 1 = yes) (enable
                                                          using the `-p' option
    Alignment score (enable using the `-s' option)
  -h / --help: Display this message.
  -n / --names: Include the read names.
  -s / --scores: Include the alignment scores.
  -p / --paired: Include pair information.
  -a / --alignments: Print the full alignments, including names and scores.
  -m / --multimatch: Print information for all available alignments in each
  -w / --nowrap: For circular references alignments may extend past the end of
     the reference or even be placed entirely past the reference for paired
     reads. With this option, the coordinates are given outside the reference
     rather than being wrapped around the end of the reference and back to the