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Description

Pad tag by specified number of adjacent bases from the read.

Command help

$ longbow pad --help
Usage: longbow pad [OPTIONS] INPUT_BAM

  Pad tag by specified number of adjacent bases from the read.

Options:
  -v, --verbosity LVL         Either CRITICAL, ERROR, WARNING, INFO or DEBUG
  -t, --threads INTEGER       number of threads to use (0 for all)  [default:
                              7]
  -o, --output-bam PATH       annotated bam output  [default: stdout]
  -m, --model TEXT            The model to use for annotation.  If not
                              specified, it will be autodetected from the BAM
                              header.  If the given value is a pre-configured
                              model name, then that model will be used.
                              Otherwise, the given value will be treated as a
                              file name and Longbow will attempt to read in
                              the file and create a LibraryModel from it.
                              Longbow will assume the contents are the
                              configuration of a LibraryModel as per
                              LibraryModel.to_json().
  -f, --force                 Force overwrite of the output files if they
                              exist.  [default: False]
  -b, --barcode-tag TEXT      The barcode tag to adjust
  -n, --new-barcode-tag TEXT  The barcode tag into which to put the adjusted
                              value.  [default: XM]
  -e, --expand INTEGER        Expand tag by specified number of bases
  --help                      Show this message and exit.


© 2021: Jonn Smith, Kiran V Garimella, Broad Institute of MIT and Harvard.