Usage: mixcr exportCloneGroups [--filter-out-of-frames] [--filter-stops]
                               [--filter-groups-with-one-chain] [--impute-germline-on-export]
                               [--dont-impute-germline-on-export]
                               [--reset-export-clone-table-splitting]
                               [--export-productive-clones-only]
                               [--export-clone-groups-for-cell-type <cell_type>]...
                               [--export-clone-groups-for-all-cell-types]
                               [--show-secondary-chain-on-export-cell-groups]
                               [--dont-show-secondary-chain-on-export-cell-groups]
                               [--export-clone-groups-sort-chains-by (Read|Molecule|Auto)]
                               [--no-header] [--drop-default-fields] [--prepend-columns]
                               [--not-covered-as-empty] [-targets] [-vHit] [-dHit] [-jHit] [-cHit]
                               [-vGene] [-dGene] [-jGene] [-cGene] [-vFamily] [-dFamily] [-jFamily]
                               [-cFamily] [-vHitScore] [-dHitScore] [-jHitScore] [-cHitScore]
                               [-vHitsWithScore] [-dHitsWithScore] [-jHitsWithScore]
                               [-cHitsWithScore] [-vHits] [-dHits] [-jHits] [-cHits] [-vGenes]
                               [-dGenes] [-jGenes] [-cGenes] [-vFamilies] [-dFamilies] [-jFamilies]
                               [-cFamilies] [-vAlignment] [-dAlignment] [-jAlignment] [-cAlignment]
                               [-vAlignments] [-dAlignments] [-jAlignments] [-cAlignments]
                               [-nFeature <gene_feature> [germline]]... [-allNFeatures
                               [<from_reference_point> <to_reference_point>]]... [-qFeature
                               <gene_feature>]... [-allQFeatures [<from_reference_point>
                               <to_reference_point>]]... [-aaFeature <gene_feature> [germline]]...
                               [-allAAFeatures [<from_reference_point> <to_reference_point>]]...
                               [-nFeatureImputed <gene_feature>]... [-allNFeaturesImputed
                               [<from_reference_point> <to_reference_point>]]... [-aaFeatureImputed
                               <gene_feature>]... [-allAAFeaturesImputed [<from_reference_point>
                               <to_reference_point>]]... [-minFeatureQuality <gene_feature>]...
                               [-allMinFeaturesQuality [<from_reference_point>
                               <to_reference_point>]]... [-allNFeaturesWithMinQuality
                               [<from_reference_point> <to_reference_point>]]...
                               [-allNFeaturesImputedWithMinQuality [<from_reference_point>
                               <to_reference_point>]]... [-avrgFeatureQuality <gene_feature>]...
                               [-allAvrgFeaturesQuality [<from_reference_point>
                               <to_reference_point>]]... [-nLength <gene_feature[,gene_feature]...>
                               [germline]]... [-allNLength [<from_reference_point>
                               <to_reference_point>]]... [-aaLength <gene_feature[,gene_feature]...
                               > [germline]]... [-allAALength [<from_reference_point>
                               <to_reference_point>]]... [-nMutations <gene_feature>
                               [(substitutions|indels|inserts|deletions)]]... [-allNMutations
                               [<from_reference_point> <to_reference_point>]
                               [(substitutions|indels|inserts|deletions)]]... [-nMutationsRelative
                               <gene_feature> <relative_to_gene_feature>
                               [(substitutions|indels|inserts|deletions)]]... [-aaMutations
                               <gene_feature> [(substitutions|indels|inserts|deletions)]]...
                               [-allAAMutations [<from_reference_point> <to_reference_point>]
                               [(substitutions|indels|inserts|deletions)]]... [-aaMutationsRelative
                               <gene_feature> <relative_to_gene_feature>
                               [(substitutions|indels|inserts|deletions)]]... [-mutationsDetailed
                               <gene_feature>]... [-allMutationsDetailed [<from_reference_point>
                               <to_reference_point>]]... [-mutationsDetailedRelative <gene_feature>
                               <relative_to_gene_feature>]... [-nMutationsCount <gene_feature[,
                               gene_feature]...> [(substitutions|indels|inserts|deletions)]]...
                               [-allNMutationsCount [<from_reference_point> <to_reference_point>]
                               [(substitutions|indels|inserts|deletions)]]... [-aaMutationsCount
                               <gene_feature[,gene_feature]...>
                               [(substitutions|indels|inserts|deletions)]]... [-allAAMutationsCount
                               [<from_reference_point> <to_reference_point>]
                               [(substitutions|indels|inserts|deletions)]]...
                               [-positionInReferenceOf <reference_point>]...
                               [-allPositionsInReference [<from_reference_point>
                               <to_reference_point>]]... [-positionOf <reference_point>]...
                               [-allPositions [<from_reference_point> <to_reference_point>]]...
                               [-defaultAnchorPoints] [-cellGroup] [-groupUniqueTagCount
                               (Molecule|Cell|Sample)]... [-groupReadCount]
                               [-uniqClonesPerChainCount] [-cloneId] [-readCount] [-rankByReads]
                               [-readFraction] [-targetSequences] [-targetQualities]
                               [-vIdentityPercents] [-dIdentityPercents] [-jIdentityPercents]
                               [-cIdentityPercents] [-vBestIdentityPercent] [-dBestIdentityPercent]
                               [-jBestIdentityPercent] [-cBestIdentityPercent] [-nMutationsRate
                               <gene_feature[,gene_feature]...>
                               [(substitutions|indels|inserts|deletions)]]... [-aaMutationsRate
                               <gene_feature[,gene_feature]...>
                               [(substitutions|indels|inserts|deletions)]]... [-geneLabel
                               <label>]... [-isotype [(primary|subclass|auto)]]... [-tagCounts]
                               [-uniqueTagCount (Molecule|Cell|Sample)]... [-uniqueTagFraction
                               (Molecule|Cell|Sample)]... [-rankByTag (Molecule|Cell|Sample)]...
                               [-hasStops <gene_feature>]... [-isOOF <gene_feature>]...
                               [-isProductive <gene_feature>]... [-biochemicalProperty
                               <gene_feature> <property>]... [-baseBiochemicalProperties
                               <gene_feature>]... [--force-overwrite] [--no-warnings] [--verbose]
                               [--help] data.(clns|clna) [table.tsv]
Export clone groups into tab delimited file. Data should be processed by `assembleCells`
      data.(clns|clna)       Path to input file with clones
      [table.tsv]            Path where to write export table.
  -o, --filter-out-of-frames Exclude clones with out-of-frame clone sequences (fractions will be
                               recalculated).
                               Default value determined by the preset.
  -t, --filter-stops         Exclude sequences containing stop codons (fractions will be
                               recalculated).
                               Default value determined by the preset.
      --filter-groups-with-one-chain
                             Exclude groups containing only one clone (fractions will be
                               recalculated).
                               Default value determined by the preset.
      --impute-germline-on-export
                             Export nucleotide sequences using letters from germline (marked
                               lowercase) for uncovered regions
      --dont-impute-germline-on-export
                             Export nucleotide sequences only from covered region
      --reset-export-clone-table-splitting
                             Reset all file splitting for output clone and/or clone group tables.
      --export-productive-clones-only
                             Export only productive clonotypes.
      --export-clone-groups-for-cell-type <cell_type>
                             Export clone groups for given cell type.
                             If selected only one cell type, export will be written in one file
                               without prefixes. If several, there will be a file for each type.
                             All cell groups that don't much specified groups will be filtered out.
                             Possible values: IGH-IGK, IGH-IGL, TRB-TRA, TRD-TRG.
      --export-clone-groups-for-all-cell-types
                             Export clone groups for all cell types.
      --show-secondary-chain-on-export-cell-groups
                             Show columns for secondary chains in export for cell groups.
      --dont-show-secondary-chain-on-export-cell-groups
                             Don't show columns for secondary chains in export for cell groups.
      --export-clone-groups-sort-chains-by (Read|Molecule|Auto)
                             How to sort clones for determination of the primary and the secondary
                               chains.
                             Read - by reads count, Molecule - by count of UMI tags, Auto - by UMI
                               if it's available, by Read otherwise
      --no-header            Don't print first header line, print only data
                               Default value determined by the preset.
      --drop-default-fields  Don't export fields from preset.
      --prepend-columns      Added columns will be inserted before default columns. By default
                               columns will be added after default columns
      --not-covered-as-empty Export not covered regions as empty text.
  -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.
Possible fields to export
      -targets               Export number of targets. For clones from all chains.
      -vHit                  Export best V hit. For clones from all chains.
      -dHit                  Export best D hit. For clones from all chains.
      -jHit                  Export best J hit. For clones from all chains.
      -cHit                  Export best C hit. For clones from all chains.
      -vGene                 Export best V hit gene name (e.g. TRBV12-3 for TRBV12-3*00). For
                               clones from all chains.
      -dGene                 Export best D hit gene name (e.g. TRBV12-3 for TRBV12-3*00). For
                               clones from all chains.
      -jGene                 Export best J hit gene name (e.g. TRBV12-3 for TRBV12-3*00). For
                               clones from all chains.
      -cGene                 Export best C hit gene name (e.g. TRBV12-3 for TRBV12-3*00). For
                               clones from all chains.
      -vFamily               Export best V hit family name (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -dFamily               Export best D hit family name (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -jFamily               Export best J hit family name (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -cFamily               Export best C hit family name (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -vHitScore             Export score for best V hit. For clones from all chains.
      -dHitScore             Export score for best D hit. For clones from all chains.
      -jHitScore             Export score for best J hit. For clones from all chains.
      -cHitScore             Export score for best C hit. For clones from all chains.
      -vHitsWithScore        Export all V hits with score. For clones from all chains.
      -dHitsWithScore        Export all D hits with score. For clones from all chains.
      -jHitsWithScore        Export all J hits with score. For clones from all chains.
      -cHitsWithScore        Export all C hits with score. For clones from all chains.
      -vHits                 Export all V hits. For clones from all chains.
      -dHits                 Export all D hits. For clones from all chains.
      -jHits                 Export all J hits. For clones from all chains.
      -cHits                 Export all C hits. For clones from all chains.
      -vGenes                Export all V gene names (e.g. TRBV12-3 for TRBV12-3*00). For clones
                               from all chains.
      -dGenes                Export all D gene names (e.g. TRBV12-3 for TRBV12-3*00). For clones
                               from all chains.
      -jGenes                Export all J gene names (e.g. TRBV12-3 for TRBV12-3*00). For clones
                               from all chains.
      -cGenes                Export all C gene names (e.g. TRBV12-3 for TRBV12-3*00). For clones
                               from all chains.
      -vFamilies             Export all V gene family anmes (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -dFamilies             Export all D gene family anmes (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -jFamilies             Export all J gene family anmes (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -cFamilies             Export all C gene family anmes (e.g. TRBV12 for TRBV12-3*00). For
                               clones from all chains.
      -vAlignment            Export best V alignment. For clones from all chains.
      -dAlignment            Export best D alignment. For clones from all chains.
      -jAlignment            Export best J alignment. For clones from all chains.
      -cAlignment            Export best C alignment. For clones from all chains.
      -vAlignments           Export all V alignments. For clones from all chains.
      -dAlignments           Export all D alignments. For clones from all chains.
      -jAlignments           Export all J alignments. For clones from all chains.
      -cAlignments           Export all C alignments. For clones from all chains.
      -nFeature <gene_feature> [germline]
                             Export nucleotide sequence of specified gene feature. If second option
                               is `germline` than will be exported corresponded sequence of the top
                               gene. It's recommended to run `findAlleles` before exporting
                               `-nFeature <gene_feature> germline` because otherwise germline
                               sequence will not incorporate allelic mutations. For clones from all
                               chains.
      -allNFeatures [<from_reference_point> <to_reference_point>]
                             Export nucleotide sequences for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allNFeatures FR3Begin FR4End` will export `-nFeature
                               FR3`, `-nFeature CDR3`, `-nFeature FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -qFeature <gene_feature>
                             Export quality string of specified gene feature. For clones from all
                               chains.
      -allQFeatures [<from_reference_point> <to_reference_point>]
                             Export quality string for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allQFeatures FR3Begin FR4End` will export `-qFeature
                               FR3`, `-qFeature CDR3`, `-qFeature FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -aaFeature <gene_feature> [germline]
                             Export amino acid sequence of specified gene feature. If second option
                               is `germline` than will be exported corresponded sequence of the top
                               gene. It's recommended to run `findAlleles` before exporting
                               `-aaFeature <gene_feature> germline` because otherwise germline
                               sequence will not incorporate allelic mutations. For clones from all
                               chains.
      -allAAFeatures [<from_reference_point> <to_reference_point>]
                             Export amino acid sequence for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allAAFeatures FR3Begin FR4End` will export `-aaFeature
                               FR3`, `-aaFeature CDR3`, `-aaFeature FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -nFeatureImputed <gene_feature>
                             Export nucleotide sequence of specified gene feature using letters
                               from germline (marked lowercase) for uncovered regions. For clones
                               from all chains.
      -allNFeaturesImputed [<from_reference_point> <to_reference_point>]
                             Export nucleotide sequence using letters from germline (marked
                               lowercase) for uncovered regions for all gene features between
                               specified reference points (in separate columns).
                             For example, `-allNFeaturesImputed FR3Begin FR4End` will export
                               `-nFeatureImputed FR3`, `-nFeatureImputed CDR3`, `-nFeatureImputed
                               FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -aaFeatureImputed <gene_feature>
                             Export amino acid sequence of specified gene feature using letters
                               from germline (marked lowercase) for uncovered regions. For clones
                               from all chains.
      -allAAFeaturesImputed [<from_reference_point> <to_reference_point>]
                             Export amino acid sequence using letters from germline (marked
                               lowercase) for uncovered regions for all gene features between
                               specified reference points (in separate columns).
                             For example, `-allAAFeaturesImputed FR3Begin FR4End` will export
                               `-aaFeatureImputed FR3`, `-aaFeatureImputed CDR3`,
                               `-aaFeatureImputed FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -minFeatureQuality <gene_feature>
                             Export minimal quality of specified gene feature. For clones from all
                               chains.
      -allMinFeaturesQuality [<from_reference_point> <to_reference_point>]
                             Export minimal quality for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allMinFeaturesQuality FR3Begin FR4End` will export
                               `-minFeatureQuality FR3`, `-minFeatureQuality CDR3`,
                               `-minFeatureQuality FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -allNFeaturesWithMinQuality [<from_reference_point> <to_reference_point>]
                             Export nucleotide sequences and minimal quality for all gene features
                               between specified reference points (in separate columns).
                             For example, `-allNFeaturesWithMinQuality FR3Begin FR4End` will export
                               `-nFeature FR3`, `-minFeatureQuality FR3`, `-nFeature CDR3`,
                               `-minFeatureQuality CDR3`, `-nFeature FR4`, `-minFeatureQuality FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -allNFeaturesImputedWithMinQuality [<from_reference_point> <to_reference_point>]
                             Export nucleotide sequences and minimal quality for all gene features
                               between specified reference points (in separate columns).
                             For example, `-allNFeaturesImputedWithMinQuality FR3Begin FR4End` will
                               export `-nFeatureImputed FR3`, `-minFeatureQuality FR3`,
                               `-nFeatureImputed CDR3`, `-minFeatureQuality CDR3`,
                               `-nFeatureImputed FR4`, `-minFeatureQuality FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -avrgFeatureQuality <gene_feature>
                             Export average quality of specified gene feature. For clones from all
                               chains.
      -allAvrgFeaturesQuality [<from_reference_point> <to_reference_point>]
                             Export average quality for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allAvrgFeaturesQuality FR3Begin FR4End` will export
                               `-avrgFeatureQuality FR3`, `-avrgFeatureQuality CDR3`,
                               `-avrgFeatureQuality FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -nLength <gene_feature[,gene_feature]...> [germline]
                             Export count of nucleotides for specified gene feature. If second
                               option is `germline` than will be count corresponding top genes,
                               VJJunction will be excluded from calculation (germline is unknown).
                               It's recommended to run `findAlleles` before exporting `-nLength
                               <gene_features> germline` because otherwise germline sequence will
                               not incorporate allelic mutations. For clones from all chains.
      -allNLength [<from_reference_point> <to_reference_point>]
                             Export nucleotides count for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allNLength FR3Begin FR4End` will export `-nLength FR3`,
                               `-nLength CDR3`, `-nLength FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -aaLength <gene_feature[,gene_feature]...> [germline]
                             Export count of amino acids for specified gene feature. If second
                               option is `germline` than will be count corresponding top genes,
                               CDR3 will be excluded from calculation (VJJunction germline is
                               unknown). It's recommended to run `findAlleles` before exporting
                               `-aaLength <gene_features> germline` because otherwise germline
                               sequence will not incorporate allelic mutations. For clones from all
                               chains.
      -allAALength [<from_reference_point> <to_reference_point>]
                             Export amino acids count for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allAALength FR3Begin FR4End` will export `-aaLength
                               FR3`, `-aaLength CDR3`, `-aaLength FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -nMutations <gene_feature> [(substitutions|indels|inserts|deletions)]
                             Extract nucleotide mutations for specific gene feature; relative to
                               germline sequence. Second parameter will filter mutations by type,
                               by default no filtering. For clones from all chains.
      -allNMutations [<from_reference_point> <to_reference_point>]
        [(substitutions|indels|inserts|deletions)]
                             Extract nucleotide mutations relative to germline sequence for all
                               gene features between specified reference points (in separate
                               columns).
                             For example, `-allNMutations FR3Begin FR4End` will export `-nMutations
                               FR3`, `-nMutations CDR3`, `-nMutations FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. Third parameter will filter
                               mutations by type, by default no filtering. For clones from all
                               chains.
      -nMutationsRelative <gene_feature> <relative_to_gene_feature>
        [(substitutions|indels|inserts|deletions)]
                             Extract nucleotide mutations for specific gene feature relative to
                               another feature. Third parameter will filter mutations by type, by
                               default no filtering. For clones from all chains.
      -aaMutations <gene_feature> [(substitutions|indels|inserts|deletions)]
                             Extract amino acid mutations for specific gene feature. Second
                               parameter will filter mutations by type, by default no filtering.
                               For clones from all chains.
      -allAAMutations [<from_reference_point> <to_reference_point>]
        [(substitutions|indels|inserts|deletions)]
                             Extract amino acid nucleotide mutations relative to germline sequence
                               for all gene features between specified reference points (in
                               separate columns).
                             For example, `-allAAMutations FR3Begin FR4End` will export
                               `-aaMutations FR3`, `-aaMutations CDR3`, `-aaMutations FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. Third parameter will filter
                               mutations by type, by default no filtering. For clones from all
                               chains.
      -aaMutationsRelative <gene_feature> <relative_to_gene_feature>
        [(substitutions|indels|inserts|deletions)]
                             Extract amino acid mutations for specific gene feature relative to
                               another feature. Third parameter will filter mutations by type, by
                               default no filtering. For clones from all chains.
      -mutationsDetailed <gene_feature>
                             Detailed list of nucleotide and corresponding amino acid mutations.
                               Format <nt_mutation>:<aa_mutation_individual>:
                               <aa_mutation_cumulative>, where <aa_mutation_individual> is an
                               expected amino acid mutation given no other mutations have occurred,
                               and <aa_mutation_cumulative> amino acid mutation is the observed
                               amino acid mutation combining effect from all other. WARNING: format
                               may change in following versions. For clones from all chains.
      -allMutationsDetailed [<from_reference_point> <to_reference_point>]
                             Detailed list of nucleotide and corresponding amino acid mutations for
                               all gene features between specified reference points (in separate
                               columns).
                             For example, `-allMutationsDetailed FR3Begin FR4End` will export
                               `-mutationsDetailed FR3`, `-mutationsDetailed CDR3`,
                               `-mutationsDetailed FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -mutationsDetailedRelative <gene_feature> <relative_to_gene_feature>
                             Detailed list of nucleotide and corresponding amino acid mutations
                               written, positions relative to specified gene feature. Format
                               <nt_mutation>:<aa_mutation_individual>:<aa_mutation_cumulative>,
                               where <aa_mutation_individual> is an expected amino acid mutation
                               given no other mutations have occurred, and <aa_mutation_cumulative>
                               amino acid mutation is the observed amino acid mutation combining
                               effect from all other. WARNING: format may change in following
                               versions. For clones from all chains.
      -nMutationsCount <gene_feature[,gene_feature]...> [(substitutions|indels|inserts|deletions)]
                             Count nucleotide mutations for specific gene feature. Second parameter
                               will filter mutations by type, by default no filtering. For clones
                               from all chains.
      -allNMutationsCount [<from_reference_point> <to_reference_point>]
        [(substitutions|indels|inserts|deletions)]
                             Count nucleotide mutations for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allNMutationsCount FR3Begin FR4End` will export
                               `-nMutationsCount FR3`, `-nMutationsCount CDR3`, `-nMutationsCount
                               FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. Third parameter will filter
                               mutations by type, by default no filtering. For clones from all
                               chains.
      -aaMutationsCount <gene_feature[,gene_feature]...> [(substitutions|indels|inserts|deletions)]
                             Count amino acid mutations for specific gene feature. Second parameter
                               will filter mutations by type, by default no filtering. For clones
                               from all chains.
      -allAAMutationsCount [<from_reference_point> <to_reference_point>]
        [(substitutions|indels|inserts|deletions)]
                             Count amino acid mutations for all gene features between specified
                               reference points (in separate columns).
                             For example, `-allAAMutationsCount FR3Begin FR4End` will export
                               `-aaMutationsCount FR3`, `-aaMutationsCount CDR3`,
                               `-aaMutationsCount FR4`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. Third parameter will filter
                               mutations by type, by default no filtering. For clones from all
                               chains.
      -positionInReferenceOf <reference_point>
                             Export position of specified reference point inside reference
                               sequences (clonal sequence / read sequence). For clones from all
                               chains.
      -allPositionsInReference [<from_reference_point> <to_reference_point>]
                             Export position inside reference sequences (clonal sequence / read
                               sequence) for all reference points between specified (in separate
                               columns).
                             For example, `-allPositionsInReference FR3Begin FR4End` will export
                               `-positionInReferenceOf FR3Begin`, -positionInReferenceOf
                               CDR3Begin`, -positionInReferenceOf CDR3End` and
                               `-positionInReferenceOf FR4End`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -positionOf <reference_point>
                             Export position of specified reference point inside target sequences
                               (clonal sequence / read sequence). For clones from all chains.
      -allPositions [<from_reference_point> <to_reference_point>]
                             Export position inside target sequences (clonal sequence / read
                               sequence) for all reference points between specified (in separate
                               columns).
                             For example, `-allPositions FR3Begin FR4End` will export `-positionOf
                               FR3Begin`, -positionOf CDR3Begin`, -positionOf CDR3End` and
                               `-positionOf FR4End`.
                             By default, boundaries will be got from analysis parameters if
                               possible or `FR1Begin FR4End` otherwise. For clones from all chains.
      -defaultAnchorPoints   Outputs a list of default reference points (like CDR2Begin, FR4End,
                               etc. see documentation for the full list and formatting). For clones
                               from all chains.
      -cellGroup             Unique cell group identifier
      -groupUniqueTagCount (Molecule|Cell|Sample)
                             Unique tag count for a cell group
      -groupReadCount        Total reads count in all cells representing this group
      -uniqClonesPerChainCount
                             Count of different clones in this group per each chain type
      -cloneId               Unique clone identifier. For clones from all chains.
      -readCount             Number of reads assigned to the clonotype. For clones from all chains.
      -rankByReads           Rank by number of reads assigned to the clonotype, i.e how many clones
                               have equal or more count. For clones from all chains.
      -readFraction          Fraction of reads assigned to the clonotype. For clones from all
                               chains.
      -targetSequences       Export aligned sequences (targets), separated with comma. For clones
                               from all chains.
      -targetQualities       Export aligned sequence (target) qualities, separated with comma. For
                               clones from all chains.
      -vIdentityPercents     V alignment identity percents. For clones from all chains.
      -dIdentityPercents     D alignment identity percents. For clones from all chains.
      -jIdentityPercents     J alignment identity percents. For clones from all chains.
      -cIdentityPercents     C alignment identity percents. For clones from all chains.
      -vBestIdentityPercent  V best alignment identity percent. For clones from all chains.
      -dBestIdentityPercent  D best alignment identity percent. For clones from all chains.
      -jBestIdentityPercent  J best alignment identity percent. For clones from all chains.
      -cBestIdentityPercent  C best alignment identity percent. For clones from all chains.
      -nMutationsRate <gene_feature[,gene_feature]...> [(substitutions|indels|inserts|deletions)]
                             Number of nucleotide mutations from germline divided by target
                               sequence size. VJJunction is excluded from calculation (germline is
                               unknown). It's recommended to run `findAlleles` before exporting
                               `-nMutationsRate` because otherwise mutations count will include
                               allelic mutations. Second parameter will filter mutations by type,
                               by default no filtering. For clones from all chains.
      -aaMutationsRate <gene_feature[,gene_feature]...> [(substitutions|indels|inserts|deletions)]
                             Number of amino acid mutations from germline divided by amino acid
                               sequence size. CDR3 is excluded from calculation (VJJunction
                               germline is unknown). It's recommended to run `findAlleles` before
                               exporting `-aaMutationsRate` because otherwise mutations count will
                               include allelic mutations. Second parameter will filter mutations by
                               type, by default no filtering. For clones from all chains.
      -geneLabel <label>     Export gene label (i.e. ReliableChain). For clones from all chains.
      -isotype [(primary|subclass|auto)]
                             Export isotype for IGH chains if it's can be distinguishable.
                               `primary` will resolve 'IgA', 'IgD', 'IgG', 'IgE', 'IgM'. `subtype`
                               will try resolve isotypes like 'IgA1' or 'IgA2'. `auto` will resolve
                               the best resolution as possible. By default `auto` will be used. For
                               clones from all chains.
      -tagCounts             All tags with counts. For clones from all chains.
      -uniqueTagCount (Molecule|Cell|Sample)
                             Unique tag count. For clones from all chains.
      -uniqueTagFraction (Molecule|Cell|Sample)
                             Fraction of unique tags (UMI, CELL, etc.) the clone or alignment
                               collected. For clones from all chains.
      -rankByTag (Molecule|Cell|Sample)
                             Rank by count of unique tags, i.e how many clones have equal or more
                               count. For clones from all chains.
      -hasStops <gene_feature>
                             Whether gene feature has stop codons inside. For clones from all
                               chains.
      -isOOF <gene_feature>  Whether gene feature is OOF. For clones from all chains.
      -isProductive <gene_feature>
                             Whether specified gene feature is productive (no stops and not OOF).
                               For clones from all chains.
      -biochemicalProperty <gene_feature> <property>
                             Biochemical property of specified gene feature normalized by AA
                               sequence size. Possible values: Hydropathy, Charge, Polarity,
                               Volume, Strength, MjEnergy, Kf1, Kf2, Kf3, Kf4, Kf5, Kf6, Kf7, Kf8,
                               Kf9, Kf10, Rim, Surface, Turn, Alpha, Beta, Core, Disorder,
                               N2Strength, N2Hydrophobicity, N2Volume, N2Surface. For clones from
                               all chains.
      -baseBiochemicalProperties <gene_feature>
                             Base biochemical properties of specified gene feature normalized by AA
                               sequence size: N2Strength, N2Hydrophobicity, N2Surface, N2Volume,
                               Charge. For clones from all chains.
