Usage: mixcr findAlleles [--export-library <path.(json|fasta)>]... [--export-alleles-mutations
                         <path.(t|c)sv>] [--result-library-name <name>]
                         [--dont-remove-unused-genes] [-O <key=value>]... [--report <path>]
                         [--json-report <path>] [--use-local-temp] [--threads <n>]
                         [--force-overwrite] [--no-warnings] [--verbose] [--help]
                         (--output-template <template.clns> | --no-clns-output) (input_file.
                         (clns|clna)|directory)...
Find allele variants in clnx.
All inputs must be fully covered by the same feature, have the same align library, the same scoring
of V and J genes and the same features to align.
      (input_file.(clns|clna)|directory)...
                             Input files or directory with files for allele search.
                             In case of directory no filter by file type will be applied.
      --output-template <template.clns>
                             Output template may contain {file_name} and {file_dir_path},
                             outputs for '-o /output/folder/{file_name}_suffix.clns input_file.clns
                               input_file2.clns' will be /output/folder/input_file_suffix.clns and
                               /output/folder/input_file2_suffix.clns,
                             outputs for '-o {file_dir_path}/{file_name}_suffix.clns
                               /some/folder1/input_file.clns /some/folder2/input_file2.clns' will
                               be /seme/folder1/input_file_suffix.clns and
                               /some/folder2/input_file2_suffix.clns
                             Resulted outputs must be uniq
      --no-clns-output       Command will not realign input clns files. Must be specified if
                               `--output-template` is omitted.
      --export-library <path.(json|fasta)>
                             Paths where to write library with found alleles and other genes that
                               exits in inputs.
                             For `.json` library will be written in reqpseqio format.
                             For `.fasta` library will be written in FASTA format with gene name
                               and feature name in description.
      --export-alleles-mutations <path.(t|c)sv>
                             Path where to write descriptions and stats for all result alleles,
                               existed and new.
                             Available columns:
                             alleleName - result allele name. If it's de nova, then before `-M` is
                               nearest known variant, M{n} is how many mutations in it and CDR3-{n}
                               is how many mutations in CDR3, at the end uniq hash.
                             geneName - gene name, the same for zygotes
                             type - gene type (Variable or Joining)
                             status - DE_NOVO: New allelic variant, that doesn't match with any
                               from the library.
                             FOUND_KNOWN_VARIANT: Known variant from the library, found by main
                               algorithm.
                             ALIGNED_ON_KNOWN_VARIANT: Not enough info for main algorithm, but the
                               main bulk of clones aligns with a known allele from the database.
                             NOT_CHANGED_AFTER_SEARCH: The found allele variant is the same as was
                               used in `align` command (clones are not changed).
                                If enoughInfo is true, then it was found by main algorithm,
                               otherwise, by aligning clones on known variants.
                             NO_CLONES_TO_SEARCH: All clones were filtered out before search (there
                               are filters by productivity and reads/UMI count).
                             COULD_NOT_BE_ALIGNED_ON_KNOWN_VARIANT: Have clones to search, but not
                               enough info for search and can't be aligned on known variant.
                             REMOVED_BECAUSE_NO_TOP_HITS_IN_RESULT_FILES: Removed because no top
                               hits in any result clone.
                             REMOVED_BECAUSE_NOT_REPRESENTED_IN_SOURCE_FILES: Not represented in
                               source clones.
                             .
                             enoughInfo - is there enough clones to search by the main algorithm.
                             mutations - list of mutations for de nova alleles.
                             varianceOf - name of nearest known gene variant for de nova allele.
                             naivesCount - how many naive clones aligned to this allele.
                             nonProductiveCount - how many non productive clones aligned to this
                               allele.
                             lowerDiversityBound - diversity of CDR3 length and different genes
                               (different J for V allele and J for V allele).
                             clonesCount - how many clones aligned to this allele.
                             totalClonesCountForGene - how many clones in all alleles of this gene
                               (after realigning).
                             clonesCountWithNegativeScoreChange - how many clones get lower score
                               after aligned to this allele.
                             filteredForAlleleSearchNaivesCount - how many naive clones aligned to
                               this allele and was used in searching.
                             filteredForAlleleSearchClonesCount - how many clones aligned to this
                               allele and was used in searching.
                             filteredForAlleleSearchClonesCountWithNegativeScoreChange - how many
                               clones get lower score after aligned to this allele and was used in
                               searching before
                             scoreDelta - stats for score change of clones after aligning to this
                               allele.
      --result-library-name <name>
                             Name for result library.
                               Default: {originalLibraryName}_with_found_alleles
      --dont-remove-unused-genes
                             Don't remove genes that weren't used in clones in the result library
  -O  <key=value>            Overrides default find alleles 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.
