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.