Usage: mixcr extend [--v-anchor <anchor_point>] [--j-anchor <anchor_point>] [--min-v-score <n>]
                    [--min-j-score <n>] [--chains <chains>] [--quality <n>] [--report <path>]
                    [--json-report <path>] [--threads <n>] [--force-overwrite] [--no-warnings]
                    [--verbose] [--help] data.(vdjca|clns|clna) extendeed.(vdjca|clns|clna)
Impute alignments or clones with germline sequences.
      data.(vdjca|clns|clna) Path to input file.
      extendeed.(vdjca|clns|clna)
                             Path where to write output. Will have the same file type.
      --v-anchor <anchor_point>
                             V extension anchor point.
                               Default value determined by the preset.
      --j-anchor <anchor_point>
                             J extension anchor point.
                               Default value determined by the preset.
      --min-v-score <n>      Minimal V hit score to perform left extension.
                               Default value determined by the preset.
      --min-j-score <n>      Minimal J hit score to perform right extension.
                               Default value determined by the preset.
  -c, --chains <chains>      Apply procedure only to alignments with specific
                               immunological-receptor chains.
                               Default: TCR
  -q, --quality <n>          Quality score value to assign imputed sequences.
                               Default: 30
  -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                               machine readable report).
  -j, --json-report <path>   JSON formatted report file.
  -t, --threads <n>          Processing threads
  -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.
