Usage: mixcr alignmentsDiff [--only-in-first <path.vdjca>] [--only-in-second <path.vdjca>]
                            [--diff-from-first <path.vdjca>] [--diff-from-second <path.vdjca>]
                            [--gene-feature <gene_feature>] [--top-hits-level <n>]
                            [--different-feature-only] [--force-overwrite] [--no-warnings]
                            [--verbose] [--help] input_file1.vdjca input_file2.vdjca [report.txt]
Calculates the difference between two .vdjca files.
      input_file1.vdjca
      input_file2.vdjca
      [report.txt]           Path where to write report. Will write to output if omitted.
      -o1, --only-in-first <path.vdjca>
                             output for alignments contained only in the first .vdjca file
      -o2, --only-in-second <path.vdjca>
                             output for alignments contained only in the second .vdjca file
      -d1, --diff-from-first <path.vdjca>
                             output for alignments from the first file that are different from
                               those alignments in the second file
      -d2, --diff-from-second <path.vdjca>
                             output for alignments from the second file that are different from
                               those alignments in the first file
  -g, --gene-feature <gene_feature>
                             Specifies a gene feature to compare.
                               Default: CDR3
  -l, --top-hits-level <n>   Number of top hits to search for a match
  -k, --different-feature-only
                             Output only those alignments that are different in terms of target
                               gene feature.
  -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.
