Usage: mixcr exportAlignmentsPretty [--top] [--gene] [--limit-before <n>] [--limit <n>] [--skip
                                    <n>] [--chains <chains>] [--cdr3-equals <seq>] [--feature
                                    <gene_feature>] [--no-feature <gene_feature>] [--read-contains
                                    <seq>] [--filter <s>] [--descriptions] [--read-ids <id>]...
                                    [--clone-ids <id>]... [--force-overwrite] [--no-warnings]
                                    [--verbose] [--help] alignments.(vdjca|clna) [output.txt]
Export verbose information about alignments.
      alignments.(vdjca|clna)
                            Path to input file with alignments.
      [output.txt]          Path where to write export. Will write to output if omitted.
  -t, --top                 Output only top hits
  -a, --gene                Output full gene sequence
  -b, --limit-before <n>    Limit number of alignments before filtering
  -n, --limit <n>           Limit number of filtered alignments; no more than N alignments will be
                              outputted
  -s, --skip <n>            Number of output alignments to skip
  -c, --chains <chains>     Filter export to a specific protein chain gene (e.g. TRA or IGH).
                              Default: ALL
  -e, --cdr3-equals <seq>   Output only alignments where CDR3 exactly equals to given sequence
  -g, --feature <gene_feature>
                            Output only alignments which contain a corresponding gene feature
      -ng, --no-feature <gene_feature>
                            Output only alignments which don't contain a corresponding gene feature
  -r, --read-contains <seq> Output only alignments where target read contains a given substring
      --filter <s>          Custom filter
  -d, --descriptions        Print read descriptions
  -i, --read-ids <id>       List of read ids to export
      --clone-ids <id>      List of clone ids to export
  -f, --force-overwrite     Force overwrite of output file(s).
      -nw, --no-warnings    Suppress all warning messages.
      --verbose             Verbose messages.
  -h, --help                Show this help message and exit.
