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o SW-score neutral (i.e. sw-scor == 0) extension of alignment at edges
o Smith-Waterman alignement can result in an segmented alignment. Such segments
are currently output in separate (e.g. SAM) output lines with the SAM FLAG bit
0x100, flagging 'secondary alignments', (inappropriately) set for all but the
highest scoring segment. Most of these alignments could be reported in one line
using the CIGAR 'N' operator designating a skipped segment of the reference.
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 For very long reads, map in segments and stitch alignment
results. Alternatively, use variable alignment band width.
o implement vectorised Smith-Waterman for (variable) alignment band.
o implement vectorised Needleman-Wunsch.
o Copy SAM/BAM header input to SAM/Bam header output.
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.
o Possibly change the maximum number of reference sequences allowed (currently
has to fit a 32 bit signed int).
o Fix annotation for doxygen. Automated build of documentation.
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