Add a Smith-Waterman fallback to support insertion/deletion errors

[LTLA]

Try to do it the usual way, and if there isn't a suitable hit, we try the fallback if indels are enabled. The "suitability" of the hit depends on the search mode:

• If we're looking for the best hit, and the best no-indel hit has any number of mismatches, then try a full SW alignment. We need to do it even if there's 1 mismatch because we need to deal with ties and any indel would be tied with a single mismatch. This could be done pretty efficiently as we can constrain the search space by using the no-indel edit distance as an upper bound.
• If we're looking for the first hit, we use the number of mismatches from the no-indel hit as an upper bound, and then we do a SW alignment based on that. If the upper bound is low enough we might be able to constrain it quite well.
• If we're looking for any hit, just do the no-indel one first and then try SW if there isn't a suitable hit. Arguably we don't really need the "first" hit, as "any" is good enough.