Options for clc_unmapped_reads

usage: clc_unmapped_reads <options>
  Extract unmapped reads from a read mapping.
  -h / --help: Display this message.
  -a <file> / --cas <file>: Specify the input cas file (required).
  -o <file> / --output <file>: Specify the output fasta or fastq file
  -l <n> / --minlength <n>: Output only sequences with a certain minimum
  -u / --unaligned: For matching reads with sufficiently long unaligned parts,
     output these parts as individual sequences. Two parts may be output if
     both ends are long enough. Must be used with the '-l' option.
  -p / --paired: Always treat the reads as paired, so if one read of a pair
     qualifies for reporting, report both reads. Cannot be used with the "-u"
  Make a fasta file with all the unmapped reads along with all read parts
  that were unaligned and has a length of at least 100 bp:
    clc_unmapped_reads -a mapping.cas -o unmapped.fasta -l 100 -u