Changes to counting multi-mappers and debugging

+ The Perl version counts each possible alignment from a multi-
  mapper separately. I'm not sure if this is desireable or not,
  but I'm making it work that way to stay consistent with the
  Perl version.

+ Took out the 'want' business and added some debug logging. If
  we're interested in looking at one exon, we can just create an
  input file that just has that one exon.