This seems to be a necessary feature for those who would rather substitute a little performance for more exhaustive mappability. A multiseed 'stitching' implementation should overcome the major caveat of long ungapped alignments.
Exhaustive SGSA Proposal:
if identity(align) < threshold
reseed = seed_locate( (align.range+1):length(read) ) # with new range to unaligned portion
ungapped_align(reseed, align=align)
end
Where the reseed is within the same SpliceGraph and SGNode additions are handled such that adjacent additions are not treated as junctions without kmer matches.
This seems to be a necessary feature for those who would rather substitute a little performance for more exhaustive mappability. A multiseed 'stitching' implementation should overcome the major caveat of long ungapped alignments.
Exhaustive SGSA Proposal:
Where the reseed is within the same SpliceGraph and SGNode additions are handled such that adjacent additions are not treated as junctions without kmer matches.