Tags each read in a BAM file

Currently supported tags:
  -suffix
  -xs
  -orig-ref
  -orig-pos
  -orig-cigar
  -junction

Usage: bamutils tag {opts} in.bamfile out.bamfile

Arguments:
  in.bamfile    The input BAM file
  out.bamfile   The name of the new output BAM file

Options:
  -suffix suff     A suffix to add to each read name

  -xs              Add the XS:A tag for +/- strandedness (req'd by Cufflinks)

  -tag tag         Add an arbitrary tag (ex: -tag XX:Z:test)

  -junction tag    Predicts junction spans from CIGAR alignment

  -orig-ref tag    Add a new tag with the original reference name (For
                   example, in a region-based BAM will be converted to
                   standard coordinates)

  -orig-pos tag    Add a new tag with the original reference pos

  -orig-cigar tag  Add a new tag with the original CIGAR alignment

  -f               Force overwriting the output BAM file if it exists