Usage: mixcr assemblePartial [--overlapped-only] [--drop-partial] [--cell-level] [-O
                             <key=value>]... [--report <path>] [--json-report <path>]
                             [--force-overwrite] [--no-warnings] [--verbose] [--help] alignments.
                             vdjca alignments.recovered.vdjca
Assembles partially aligned reads into longer sequences.
      alignments.vdjca       Path to input alignments file.
      alignments.recovered.vdjca
                             Path where to write recovered alignments.
  -o, --overlapped-only      Write only overlapped sequences (needed for testing).
                               Default value determined by the preset.
  -d, --drop-partial         Drop partial sequences which were not assembled. Can be used to reduce
                               output file size if no additional rounds of `assemblePartial` are
                               required.
                               Default value determined by the preset.
      --cell-level           Overlap sequences on the cell level instead of UMIs for tagged data
                               with molecular and cell barcodes.
                               Default value determined by the preset.
  -O  <key=value>            Overrides default parameter values.
  -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                               machine readable report).
  -j, --json-report <path>   JSON formatted report file.
  -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.
