Options for clc_mapper_legacy 

usage: clc_mapper_legacy <options>
  Map some reads to some reference sequences.
Options:
  -h / --help: Display this message
  -q / --reads: The files following this option are read files. (may be used
     several times)
  -d / --reference: The files following this option are reference files. Fasta
     and GenBank formats are allowed. (may be used several times)
  -o <file> / --output <file>: Output mapping result to a cas file (required)
  -i <file1> <file2> / --interleave <file1> <file2>: Interleave the sequences
     in two files immediately following the "-i" option, alternating between
     the two files when reading the sequences. Only valid for read files. (may
     be used several times).
  -x <n> / --mismatchcost <n>: Set the mismatch cost (integer range 1 to 3, default 2)
  -g <n> / --gapcost <n>: Set the gap cost (integer range 1 to 3, default 3)
  -e <n> / --deletioncost <n>: Set the deletion cost in which case the gap cost
     setting only applies to insertions. (integer range 1 to 3, default 3)
  -c / --colorspace: Use color space when aligning.
  -y <n> / --colorerrorcost <n>: Set the cost of an error in a color when using
     color space. Can only be used with the "-c" option. (range 1 to 3, default
     3)
  -r <mode> / --repeat <mode>: Set the behavior for reads that match more than
     once, i.e. ignore such reads or place them randomly among the valid
     locations (ignore / random) (default random)
  -l <n> / --lengthfraction <n>: Set the fraction of the read that must match. A
     real number between 0.0 and 1.0 (default 0.5).
  -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 (default 0.8).
  -p <par> / --paired <par>: Set the paired read mode for the read files
     following this option. (may be used several times)
     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.
     To explicitly say that the following reads are not paired, use "no" for
     par, i.e. "-p no".
     For paired end reads split in two files, use the -i option.
  -m <n> / --memory <n>: Set the maximum amount of memory to use as a fraction
     of the available memory (default is 1.0).
  -t <n> / --maxalign <n>: Set the maximum number of alignments to report for
     each read (default is 1).
  -a <mode> / --alignmode <mode>: Set the alignment mode to one of the
     following:
       local: perform local alignment (default)
       global: perform global alignment
       semi-global: perform semi-global alignment
  -f / --forwardonly: Only match reads in the forward direction
  -b / --backwardonly: Only match reads in the backward direction
  --cpus <n>: Set the number of cpus to use.
  --no-progress: Disable progress bar.
Examples:
  Map reads in a single file to a single file with reference sequences:
    clc_mapper_legacy -o mapping.cas -q reads.fasta -d reference.fasta
  Map reads from two unpaired runs and a paired end run split across two
  files. Use two reference sequences:
    clc_mapper_legacy -o mapping.cas -q unpaired1.fasta unpaired2.fasta
                         -p fb ss 180 250 -i paired_1.qf paired_2.qf -d
                         reference1.gb reference2.gb