Options for clc_submapping 

usage: clc_submapping <options>
  Extract part of a read mapping into a new cas file.
Options:
  -h / --help: Display this message
  -a <file> / --cas <file>: Set the input cas file (required).
  -o <file> / --output <file>: Set the output cas file (required).
  -d <n> / --reffile <n>: Restrict matches to a single reference file denoted
     by its number.
  -s <n> / --refseq <n>: Restrict matches to a single reference sequence
     denoted by its number.
  -r <n> / --reflength <n>: Restrict matches to reference sequences of a given
     minimum length.
  -q <n> / --readfile <n>: Restrict matches to a single read file (or two if
     interlaced) denoted by its number.
  -b <m-n> / --subsequence <m-n>: Restrict matches to a position range. The
      positions start from 1. The '-s' option must also be specified if more
      than one reference sequence is present in the assembly.
  -u / --unique: Restrict to uniquely placed matches.
  -l <n> / --minlength <n>: Restrict to matches where a minimum of n read
     positions are aligned (but not necessarily matching).
  -f <file> / --readoutput <file>: Output file for reads (fasta or fastq format
     depending on file name). Only matching reads are output. With this option
     the output assembly refers to this read file instead of the original read
     files. When both paired and unpaired reads are output, use the -e option to
     speicify the name of the paired read file.
  -e <file> / --pairreadoutput <file>: Output file for paired reads when both
     paired and unpaired reads are output. I.e. when the assembly has both paired
     and unpaired reads, the -f option is used, and the -p and -q options are not
     used.
  -g <file> / --refoutput <file>: Output file for references. With this option
     the output assembly refers to this reference file instead of the original
     reference files.
  -p / --paired: Keep read pairs together when making read output file. Should
     be used when the reads are from a paired end experiment, but were assembled
     as unpaired. If assembled as paired, the pairs will automatically be kept
     together. May only be used with the '-f' option.
Examples:
  Make a read mapping with only reference sequence two of an existing read
  mapping. Also make a new file for the reads matching this sequence:
    clc_submapping -a mapping.cas -o new_mapping.cas -s 2 -f new_reads.fasta
  The same but only the first 100,000 positions of the reference sequence and
  also make a file for the new partial reference sequence
    clc_submapping -a mapping.cas -o new_mapping.cas -s 2 -b 1-100000
                                  -f new_reads.fasta -g new_ref.fasta
  Make an assembly without ambiguously placed reads:
    clc_submapping -a mapping.cas -o new_mapping.cas -u