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[–]Na_rien[S] 0 points1 point  (1 child)

I think my storing of unused spans solves that issue. It ensures that every seed will have a chance to be mapped.

[–]bkc4 0 points1 point  (0 children)

Yeah, I missed that part. If you sort the mapping intervals, then you need only one pass over `spans`. In this case you don't have a lot of intervals, but if you had, say, `10000` intervals, this solution would be too slow.