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OpenReadout

link

link groups files that measured the same sample across instruments and formats, and gives the evidence and a confidence for every link. It reads headers only.

openreadout link [OPTIONS] [PATH]...

Evidence includes sample ids, barcodes, plate wells, conversions that name their source file, and the same acquisition stored twice.

Flags

  • --no-recursive: only the top level of directory arguments. By default directories are walked.
  • --min-confidence low|medium|high: links below this confidence are listed but do not join groups. Default medium.
  • --max-shared N: an identifier shared by more data sets than this counts as weak evidence. Default 12.
  • --formats IDS: only data sets of these format ids.
  • --from-index INDEX_DIR: add the data sets an index selects.
  • --query QUERY: the index query for --from-index.
  • --json: print the JSON wrapper instead of text.

Examples

Terminal window
openreadout link share/
openreadout link share/ --min-confidence high --json
openreadout link --from-index /lab/index --query "sample~P0042"

How the evidence is weighed: Batch tables guide.

JSON

link.

Run openreadout link --help for the full help of your installed version.