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) Options: -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 match. -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 start.