Options for clc_cas_to_sam

usage: clc_cas_to_sam <options>
  Convert a cas file to sam or bam format.
  -h / --help: Display this message
  -a <file> / --cas <file>: Set the input cas file (required).
  -o <file> / --output <file>: Set the output sam or bam file. Sam format is
      assumed unless the file ends with ".bam" or ".BAM" (required).
  -f <offset> / --qualityoffset <offset>: Set the ascii offset value in fastq
      files (default is 64).
  -u / --discardunmapped: Discard the unmapped reads
  -m / --multimatch: Output all available alignments in each match
  --no-progress: Disable progress bar.
  Convert a cas file to bam format:
    clc_cas_to_sam -a assembly.cas -o assembly.bam