Options for clc_mapping_info
usage: clc_mapping_info [options] <cas file> Print information about a read mapping. Options: -h / --help: Display this message. -c / --coverage: Show more detailed coverage information -x <n> / --maxcoverage <n>: Set the maximum coverage for the detailed coverage information (from the "-c" option). -s / --skipcontigs: Skip contig specific information -n / --correct: Also show coverage corrected for ambiguous residues in reference sequences. -d <file> / --coveragefile <file>: Output coverage as a function of position for each reference sequence to different files called <file>.001.dat, <file>.002.dat, etc. -p <par> / --paired <par>: Set the paired read mode. par consists of four strings: <mode> <dist_mode> <min_dist> <max_dist> mode is ff, fb, bf, bb and sets the relative orientation of read one and two in a pair (f = forward, b = backward). dist_mode is ss, se, es, ee and sets the place on read one and two to measure the distance (s = start, e = end). A typical use would be "-p fb ss 180 250" which means that the reads are inverted and pointing towards each other. The distance includes both the reads and the sequence between them. The distance may be between 180 and 250, both included. Only read pairs satisfying these criteria are counted in the distance statistics. If both the minimum and maximum distances are set to zero, the actual paired status of the reads is used to determine whether they pair. -q <file> / --pairedfile <file>: Output file for distance histogram for paired end data. -i <n> / --individualfile <n>: Only generate info for one of the read files specified by its number. -f / --fast: No coverage information for a fast result. -m / --mismatch: Show counts of mismatches, insertions and deletions. -e <n> / --endinfo <n>: Show information about the contig nucleotides around the ends of the reads up to the given distance.