`mixcr exportReportsTable`

Export all reports from any MiXCR binary file (.vdjca, .clns, .clna and .shmt) in tabular form.

mixcr exportReportsTable 
    [--with-upstreams] 
    [--preset <preset>] 
    [--preset-file <presetFile>] 
    [--no-header] 
    [<exportField>]...
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    (data.(vdjca|clns|clna|shmt)|directory)... [report.tsv]

Command line options:

(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.
--with-upstreams: Export upstream reports for sources of steps with several inputs, like findShmTrees.
-p, --preset <preset>: Specify preset of export fields. Possible values: min, full. By default 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.

Export fields

-fileName: File name as it was specified in command exportReportsTable.
-MiXCRVersion: Version of MiXCR.
-inputFilesAlign: Input files on align command.
-totalReads: Count of reads in original data.
-patternMatchedReads: Percentage of reads that match pattern.
-overlapped: Percentage of overlapped reads.
-overlappedAndAligned: Percentage of overlapped and aligned reads.
-alignmentsFailed: Percentage of reads that not aligned because of different reasons (columns for each reason).
-successAligned: Percentage of aligned reads.
-readsWithChain: Percentage of reads aligned on specific chain. Will be exported all found chains.
-inputFileAssemble: Input files on assemble command.
-readsClusteredInCorrection: Reads pre-clustered due to the similar VJC-lists, percent of used.
-droppedNoClonalSeq: Reads dropped due to the lack of a clone sequence, percent of total.
-droppedShortSeq: Reads dropped due to a too short clonal sequence, percent of total.
-droppedLowQual: Reads dropped due to low quality, percent of total.
-droppedFailedMapping: Reads dropped due to failed mapping, percent of total
-inputFileAssembleContigs: Input files on assembleContigs command.
-totalClonotypes: Total clonotypes after assembleContigs command if it was run, assemble otherwise.
-readsUsedInClonotypes: Reads used in clonotypes after assembleContigs command if it was run, assemble otherwise.
-clonesWithChain: Percentage of clones aligned on specific chain (assemble command). Will be exported all found chains.
-foundAllelesCount: Count of found alleles.
-foundTreesCount: Count of found trees.
-cloneInTreesCount: Count of uniq clones that was included in trees.