bamutils / renamepair

Postprocesses a BAM file to rename pairs that have an extra /N value

Some aligners output paired end reads with names ending in /1 or /2 to signify
where the read came from in a paired end experiment. This can cause problems
with downstream analysis packages that expect paired end reads to have the
exact same name.

Usage: bamutils renamepair {opts} inbamfile outbamfile

  -f           Force overwriting an existing outfile
  -delim val   The trailing delimiter to use (default '/')