Version 0.3.1

0.3.1

• The various bedGraph files didn't previously have a "track" line. The UCSC
  Genome Browser requires this, so bedGraph files produced will now contain
  it. It should be noted that this is the very minimal line required. Bison
  does not provide facilities for making these changes, users need to edit
  things manually or use external programs for this. It should also be noted
  that any changes to the "track" or other header lines should be made after
  all processing with Bison is complete.
• Add conversion scripts for import into MethylSeekR, BiSeq, and BEAT.
• Revamped how bison_markduplicates works. The 3' coordinates are now
  ignored, soft-clipped bases on the 5' end are now incorporated in
  determining the 5' coordinate and methylation calls are also used in
  determining if reads/pairs are duplicates. This should be a much more
  robust (though more resource intensive) method than that previously used.
  Whereas the previous version kept unmarked the read/pair with the highest
  MAPQ, this one will do that for the read/pair with the highest summed phred
  score (a la picard).