Options for clc_filter_matches
usage: clc_filter_matches <options>
Remove matches from a read mapping if they do not live up to some given criteria.
Options:
-h / --help: Display this message.
-a <file> / --cas <file>: Set the input cas file (required).
-o <file> / --output <file>: Set the output cas file (required).
-l <n> / --lengthfraction <n>: Set the fraction of the read that must match. A
real number between 0.0 and 1.0 (required).
-s <n> / --similarity <n>: Set the limit for the similarity in the fraction
of the read that must match (according to "-l" option). A real number
between 0.0 and 1.0 (required).
-p / --paired: Only include paired reads in the output