Usage: mixcr postanalysis overlap --default-downsampling (<type>|none) --default-weight-function
                                  (<read>|<Tag>|none) [--criteria <s>] [--factor-by <meta>[,
                                  <meta>...]]... [--only-productive] [--drop-outliers] [--chains
                                  <chain>[,<chain>...]]... [--metadata <path>] [--group <group>[,
                                  <group>...]]... [--tables <path.(tsv|csv)>] [--preproc-tables
                                  <path.(tsv|csv)>] [-O <key=value>]... [--force-overwrite]
                                  [--no-warnings] [--verbose] [--help] (cloneset.(clns|clna)
                                  |directory)... result.json[.gz]
Overlap analysis
      (cloneset.(clns|clna)|directory)...
                           Paths to input clnx files or to directories with clnx files. Files in
                             directories will not be filtered by extension.
      result.json[.gz]     Path where to write postanalysis result.
      --default-downsampling (<type>|none)
                           Default downsampling applied to normalize the clonesets. Possible
                             values:
                           count-[reads|TAG|molecule]-[auto|min|fixed-<number>]
                            top-[reads|TAG|molecule]-[<number>]
                            cumtop-[reads|TAG|molecule]-[percent]
      --default-weight-function (<read>|<Tag>|none)
                           Default clonotype weight function
      --criteria <s>       Overlap criteria. Defines the rules to treat clones as equal. It allows
                             to specify gene feature for overlap (nucleotide or amino acid), and
                             optionally use V and J hits.
                           Examples: `CDR3|AA|V|J` (overlap by a.a. CDR3 and V and J),
                             `VDJRegion|AA` (overlap by a.a. `VDJRegion`), `CDR3|NT|V` (overlap by
                             nt CDR3 and V).
                             Default: CDR3|AA|V|J
      --factor-by <meta>[,<meta>...]
                           Pools samples with the same values of specified metadata columns and
                             performs overlap between such pooled samples
      --only-productive    Filter out-of-frame sequences and sequences with stop-codons.
      --drop-outliers      Drop samples which are below downsampling value as computed according to
                             specified default downsampling option.
      --chains <chain>[,<chain>...]
                           Limit analysis to specific chains (e.g. TRA or IGH) (fractions will be
                             recalculated). Possible values (multiple values allowed): TRA, TRD,
                             TRAD (for human), TRG, IGH, IGK, IGL
      --metadata <path>    Metadata file in a tab- (`.tsv`) or comma- (`.csv`) separated form. Must
                             contain `sample` column which matches names of input files. Optionally
                             may have `chains` column.
      --group <group>[,<group>...]
                           Metadata column used to group samples into isolation groups;
                             postanalysis will be performed in each of the groups separately. It is
                             possible to specify several isolation groups.
      --tables <path.(tsv|csv)>
                           Results output path.
                           By default, will be `{outputDir}/{outputFileName}.tsv`.
                           For each `chain` and `metric` will be generated file with path `{dir}/
                             {fileName}.{metric}.{chain}.(tsv|csv)`
      --preproc-tables <path.(tsv|csv)>
                           Output path for the preprocessing summary tables (filtering and
                             downsampling)
                           By default, will be `{outputDir}/{outputFileName}.preproc.tsv`.
                           For each `chain` will be generated file with path `{dir}/{fileName}.
                             {chain}.(tsv|csv)`
  -O  <key=value>          Overrides default postanalysis settings
  -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.
