Fix uint64_t underflow

[bkille]

This fixes an issue where the alignment step would crash with

[wfmash::align::computeAlignments] aligned 21.03% @ 3.01e+06 bp/s elapsed: 00:00:01:31 remain: 00:00:05:41
terminate called after throwing an instance of 'std::length_error'
  what():  basic_string::_M_create

This PR fixes this specific case, but there are still other cases where underflow might be possible due to using uint64_t. I'd be in favor of converting all of the uint64_t to int64_t, since afaik there isn't any bitmasking and the 63 bits are sufficient for the coordinates.