Usage: mixcr findShmTrees [--v-gene-names <gene_name>]... [--j-gene-names <gene_name>]...
                          [--cdr3-lengths <n>]... [--min-count <n>] [--productive-only]
                          [--dont-combine-tree-by-cells] [-O <key=value>]... [--report <path>]
                          [--json-report <path>] [--use-local-temp] [--threads <n>]
                          [--force-overwrite] [--no-warnings] [--verbose] [--help] (input_file.
                          clns|directory)... output_file.shmt
Builds SHM trees.
All inputs must be fully covered by the same feature, have the same library produced by
`findAlleles`, the same scoring of V and J genes and the same features to align.
      (input_file.clns|directory)...
                             Paths to clns files or to directory with clns files that was processed
                               by 'findAlleles' command.
                             In case of directory no filter by file type will be applied.
      output_file.shmt       Path where to write output trees
      --v-gene-names <gene_name>
                             List of VGene names to filter clones
      --j-gene-names <gene_name>
                             List of JGene names to filter clones
      --cdr3-lengths <n>     List of CDR3 nucleotide sequence lengths to filter clones
      --min-count <n>        Filter clones with counts great or equal to that parameter
      --productive-only      Build trees only on productive clones (no stop codons in all features
                               and no out of frame in CDR3)
      --dont-combine-tree-by-cells
                             In case of data with cell groups, will not combine trees by cells.
  -O  <key=value>            Overrides default build SHM 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.
      --use-local-temp       Put temporary files in the same folder as the output files.
  -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.
