Usage: mixcr exportReportsTable [--without-upstreams] [--preset <preset>] [--preset-file
                                <presetFile>] [--no-header] [-fileName] [-MiXCRVersion]
                                [-totalReads] [-totalClonotypes] [-clonesWithChain]
                                [-readsUsedInClonotypes] [-align.inputFiles] [-align.
                                patternMatchedReads] [-align.overlapped] [-align.
                                overlappedAndAligned] [-align.alignmentsFailed] [-align.
                                successAligned] [-align.readsWithChain] [-align.readsCoverage]
                                [-refineTags.outputDiversity] [-refineTags.outputReadsCount]
                                [-refineTags.numberOfGroupsAccepted] [-refineTags.
                                totalWeightAccepted] [-refineTags.effectiveThreshold] [-assemble.
                                inputFile] [-assemble.readsClusteredInCorrection] [-assemble.
                                droppedReads] [-assemble.coreReads] [-assemble.preCloneAssembler.
                                inputGroups] [-assemble.preCloneAssembler.preClones] [-assemble.
                                preCloneAssembler.assemblingFeatureSequencesInZeroPreClones]
                                [-assemble.preCloneAssembler.unassignedAlignments]
                                [-assembleContigs.inputFiles] [-assembleCells.inputFiles]
                                [-assembleCells.numberOfGroups] [-assembleCells.
                                unassignedClonotypes] [-assembleCells.invalidGroups]
                                [-assembleCells.groupsWithTooMatchClones] [-assembleCells.
                                cloneContamination] [-assembleCells.contaminatedCells]
                                [-assembleCells.cellsNotIncludedBecauseContamination]
                                [-assembleCells.cellBarcodesWithFoundGroups] [-findAlleles.
                                inputFiles] [-findAlleles.found] [-findAlleles.deNova]
                                [-findAlleles.notEnoughInformation] [-findTrees.inputFiles]
                                [-findTrees.treesCount] [-findTrees.cloneInTrees]
                                [--force-overwrite] [--no-warnings] [--verbose] [--help] (data.
                                (vdjca|clns|clna|shmt)|directory)... [report.tsv]
Export reports from files in tabular format.
      (data.(vdjca|clns|clna|shmt)|directory)...
                             Path to input files or directories.
                             In case of directory no filter by file type will be applied.
      [report.tsv]           Path where to write reports. Print in stdout if omitted.
      --without-upstreams    Don't export upstream reports for sources of steps with several
                               inputs, like `findShmTrees`.
  -p, --preset <preset>      Specify preset of export fields. Possible values: min, full.
      -pf, --preset-file <presetFile>
                             Specify preset file of export fields
      --no-header            Don't print first header line, print only data
  -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
      -fileName              File name as it was specified in command `exportReportsTable`.
      -MiXCRVersion          Version of MiXCR.
      -totalReads            Count of reads in original data.
      -totalClonotypes       Total clonotypes after `assembleContigs` command if it was run,
                               `assemble` otherwise.
      -clonesWithChain       Percentage of clones aligned on specific chain (`assemble` command).
                               Will be exported for all found chains.
      -readsUsedInClonotypes Reads used in clonotypes after `assembleContigs` command if it was
                               run, `assemble` otherwise.
      -align.inputFiles      Input files on `align` command.
      -align.patternMatchedReads
                             Percentage and absolute of reads that match pattern.
      -align.overlapped      Percentage and absolute of overlapped paired-end reads.
      -align.overlappedAndAligned
                             Percentage and absolute of overlapped and aligned reads (in any order).
      -align.alignmentsFailed
                             Percentage and absolute of reads that not aligned because of different
                               reasons (columns for each reason).
      -align.successAligned  Percentage and absolute of aligned reads.
      -align.readsWithChain  Percentage and absolute of reads aligned on specific chain. Will be
                               exported for all found chains.
      -align.readsCoverage   Percentage of reads that fully cover feature. Will be exported for all
                               calculated features.
      -refineTags.outputDiversity
                             Output diversity of tag as absolute and percentage from input
                               diversity. Will be exported for all tags.
      -refineTags.outputReadsCount
                             Output reads for refine tag as absolute and percentage from input
                               reads. Will be exported for all tags.
      -refineTags.numberOfGroupsAccepted
                             Number of unique groups of tags after filtering as absolute and
                               percentage from initial number of unique groups of tags after
                               correction.
      -refineTags.totalWeightAccepted
                             Total number of groups of tags after filtering as absolute and
                               percentage from initial number of total number of input groups after
                               correction.
      -refineTags.effectiveThreshold
                             Reads per group threshold used for filtering. Will be exported for
                               every step that used it.
      -assemble.inputFile    Input files on `assemble` command.
      -assemble.readsClusteredInCorrection
                             Reads pre-clustered due to the similar VJC-lists as absolute and
                               percentage of used reads.
      -assemble.droppedReads Reads dropped as absolute and percentage of total input reads.
                             noClonalSeq - due to the lack of a clone sequence.
                             shortSeq - due to a too short clonal sequence.
                             lowQual - due to low quality.
                             failedMapping - due to failed mapping.

      -assemble.coreReads    Number of reads used as a core for clustering as absolute and
                               percentage of reads used for clustering.
      -assemble.preCloneAssembler.inputGroups
                             Pre-clone assembler: number of groups defined by unique barcodes
                               combination. In case of single-cell UMI-barcoded library equals to
                               unique CellId+UMI groups.
      -assemble.preCloneAssembler.preClones
                             Number of pre-clonotypes per group and total.
      -assemble.preCloneAssembler.assemblingFeatureSequencesInZeroPreClones
                             Number of assembling feature sequences in groups with zero
                               pre-clonotypes.
      -assemble.preCloneAssembler.unassignedAlignments
                             Unassigned alignments as absolute and percentage of input alignments
      -assembleContigs.inputFiles
                             Input files on `assembleContigs` command.
      -assembleCells.inputFiles
                             Input files on `assembleCells` command.
      -assembleCells.numberOfGroups
                             Number of formed groups of clones
      -assembleCells.unassignedClonotypes
                             Number of clones that haven't been included in any group
      -assembleCells.invalidGroups
                             Count of groups with incompatible chains
      -assembleCells.groupsWithTooMatchClones
                             Groups with more than two chains of the same type
      -assembleCells.cloneContamination
                             Clones that possibly are contamination
      -assembleCells.contaminatedCells
                             Cells with detected and resolved contamination
      -assembleCells.cellsNotIncludedBecauseContamination
                             Cell barcodes filtered out because it's clones are contamination
      -assembleCells.cellBarcodesWithFoundGroups
                             Cell barcodes used in result groups
      -findAlleles.inputFiles
                             Input files on `findAlleles` command.
      -findAlleles.found     Count of found alleles.
      -findAlleles.deNova    Count of de nova found alleles.
      -findAlleles.notEnoughInformation
                             Count of genes that had not enough information to reliably determinate
                               allele variant.
      -findTrees.inputFiles  Input files on `findAlleles` command.
      -findTrees.treesCount  Count of found trees.
      -findTrees.cloneInTrees
                             Count of uniq clones that was included in trees as absolute and
                               percentage from input clones.
