Usage: mixcr filterAlignments [--chains <chains>] [--contains-feature <gene_feature>]
                              [--cdr3-equals <seq>] [--chimeras-only] [--limit <n>]
                              [--force-overwrite] [--no-warnings] [--verbose] [--help] alignments.
                              vdjca alignments.filtered.vdjca
Filter alignments.
      alignments.vdjca      Path to input file with alignments.
      alignments.filtered.vdjca
                            Path where to write filtered alignments.
  -c, --chains <chains>     Specifies immunological protein chain gene for an alignment. If many,
                              separated by ','. Available genes: IGH, IGL, IGK, TRA, TRB, TRG, TRD.
                              Default: ALL
  -g, --contains-feature <gene_feature>
                            Include only those alignments that contain specified feature.
  -e, --cdr3-equals <seq>   Include only those alignments which CDR3 equals to a specified sequence.
  -x, --chimeras-only       Output only chimeric alignments.
  -n, --limit <n>           Maximal number of reads to process
  -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.
