Usage: mixcr refineTagsAndSort [--power <d>] [--substitution-rate <d>] [--indel-rate <d>]
                               [--min-quality <n>] [--max-substitutions <n>] [--max-indels <n>]
                               [--max-errors <n>] [--memory-budget <n>] [--set-whitelist
                               <key=value>] [--reset-whitelist <tag_name>]
                               [--dont-correct-tag-with-name <tag_name>] [--dont-correct-tag-type
                               (Molecule|Cell|Sample)] [--report <path>] [--json-report <path>]
                               [--use-local-temp] [--force-overwrite] [--no-warnings] [--verbose]
                               [--help] alignments.vdjca alignments.corrected.vdjca
Applies error correction algorithm for tag sequences and sorts resulting file by tags.
      alignments.vdjca       Path to input alignments
      alignments.corrected.vdjca
                             Path where to write corrected alignments
  -p, --power <d>            This parameter determines how thorough the procedure should eliminate
                               variants looking like errors.
                             Smaller value leave less erroneous variants at the cost of
                               accidentally correcting true variants.
                             This value approximates the fraction of erroneous variants the
                               algorithm will miss (type II errors).
                               Default value determined by the preset.
  -s, --substitution-rate <d>
                             Expected background non-sequencing-related substitution rate.
                               Default value determined by the preset.
  -i, --indel-rate <d>       Expected background non-sequencing-related indel rate.
                               Default value determined by the preset.
  -q, --min-quality <n>      Minimal quality score for the tag.
                             Tags having positions with lower quality score will be discarded, if
                               not corrected.
                               Default value determined by the preset.
      --max-substitutions <n>
                             Maximal number of substitutions to search for.
                               Default value determined by the preset.
      --max-indels <n>       Maximal number of indels to search for.
                               Default value determined by the preset.
      --max-errors <n>       Maximal number of substitutions and indels combined to search for.
                               Default value determined by the preset.
      --memory-budget <n>    Memory budget in bytes. Default: 4Gb
      --set-whitelist <key=value>
                             Sets the whitelist for a specific tag to guide the tag refinement
                               procedure.
                             Usage: --set-whitelist CELL=preset:737K-august-2016 or --set-whitelist
                               UMI=file:my_umi_whitelist.txt .
      --reset-whitelist <tag_name>
                             Resets the whitelist for a specific tag so that unguided refinement
                               procedure will be applied for it
      --dont-correct-tag-with-name <tag_name>
                             Don't correct alignments for tag
      --dont-correct-tag-type (Molecule|Cell|Sample)
                             Don't correct alignments for tag type
  -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.
  -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.
