handle ambiguity codes in XN and MD

Two changes to more consistently handle ambiguity codes:
- The MD field correctly reports any ambiguity codes (looks ugly, but is
  correct); this includes other codes than N.
- The XN field reports the count of ambiguity in this alignment and in
  the mate's alignment.  The symmetry gained by that makes it possible
  to filter on the value of XN without disrupting mate pairs.