Require the alignment to start and end on a specific contig

[nh13]

To require it to start on the contig, assign a starting score for all other contigs of MIN_SCORE. To require to end on the contig, only look at alignments ending on that contig (in the traceback).

This would be useful if we know a prior among a number of contigs that the reads should align to it, but want to allow the alignment to jump to other contigs (i.e. contaminants) if the alignments to the latter overcomes the jump score...