TODO

TODO list
---------

- pairwiseAlignment() is broken on BString objects:

    pairwiseAlignment(BString("xxYYxx"), BString("YY"))
    # Global PairwiseAlignmentsSingleSubject (1 of 1)
    # pattern: xxYYxx
    # subject: --YY--
    # score: -34.03641
    pairwiseAlignment(BString("YYYYYY"), BString("YY"))
    # Global PairwiseAlignmentsSingleSubject (1 of 1)
    # pattern: --YYYYYY
    # subject: YY------
    # score: -52

  This 2nd alignment deosn't look like the best one.

  Furthermore, aligning the 2 patterns above with a single call to
  pairwiseAlignment() gives a different alignment for the 2nd pattern:

    pa <- pairwiseAlignment(BStringSet(c("xxYYxx", "YYYYYY")), BString("YY"))
    pa[1]
    # Global PairwiseAlignmentsSingleSubject (1 of 1)
    # pattern: xxYYxx
    # subject: --YY--
    # score: -34.03641
    pa[2]
    # Global PairwiseAlignmentsSingleSubject (1 of 1)
    # pattern: YYYYYY
    # subject: Y----Y
    # score: -24.03641

  This 2nd alignment looks correct now.

- Extend pairwiseAlignment to return the set of maximum alignments, rather
  than just one element from that set.