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.