o Where there are too many possible alignments, use mate info to reduce
  number of alignments.

o sample insert distribution differentiated by relative read orientation.

o SW-score neutral (i.e. sw-scor == 0) extension of alignment at edges

o for very long reads, segment and stitch. Alternatively, use variable alignment band width.

o implement vectorised Smith-Waterman for (variable) alignment band.

o implement vectorised Needleman-Wunsch.

o on SAM/BAM input copy header to output along with command line (@CL) and
  SMALT software version used.

o support gzipped output (zlib)

o Adjust -s automatically when k-mer positions don't fit in 32-bit unsigned
  integer (indexing a large reference). 

o Possibly change the maximum number of reference sequences allowed (currently 
  has to fit a 32 bit signed int).

o Use of the '-d' option currently breaks recommendation in SAM/BAM spec that only 
  one record per segment should have the secondary alignment flag bit (0x100) unset.

o comma separates list in the argument of command line options '-S' and '-f'
  are truncated when they are reported.

o Flags of SAM/BAM input lines are currently ignored/overwritten. For
  example, an orphaned read of a mate pair (SAM input) will be output
  as a single read.
