Usage: update_mapq [OPTIONS]

  Update supplementary read MAPQ score after remapping.

Options:
  --source_path PATH    Alignment file where supplementary reads should be
                        updated with new MAPQ scores  [required]
  --remapped_path PATH  Alignment file that contains reads that have been
                        remapped and contain an updated MAPQ score  [required]
  --output_path PATH    Write all alignments in original_path to this
                        location. Supplementary reads will take the MAPQ score
                        as determined by remapping to the alignment file at
                        `remapped_path`  [required]
  --version             Show the version and exit.
  --help                Show this message and exit.