Options for clc_sam_to_cas

usage: clc_sam_to_cas <options>
  Convert a read mapping in sam or bam format to a cas file.
  -h / --help: Display this message
  -a <file> / --input <file>: Set the input sam or bam file (required).
  -o <file> / --output <file>: Set the output cas file (required).
  -q <file> / --reads <file>: Set the output unpaired read file.
  -p <file> / --pairedreads <file>: Set the output paired read file.
  -d <file> / --reference <file>: Set the existing reference file (required, may
      be used several times).
  -f / --fast: Skip check for dispersed multi hits
  -n / --names: Do not insist that the reference sequence names match, just
      their lengths.
  --no-progress: Disable progress bar.
  Convert a paired sam file to cas format:
    clc_sam_to_cas -a mapping.sam -o mapping.cas -q unpaired_reads.fa
                                       -p paired_reads.fa -d ref1.fa -d ref2.fa
  The sam file contains read sequences but not reference sequences. Thus, the
  files ref1.fa and ref2.fa containing the references must exist already. They
  must also be specified in the same order as the references appear in the sam
  file. The read files are created from the sam file along with the new cas
  file. Paired and unpaired reads are put in separate files that only need to
  be specified in the cas such reads are present in the sam file