NeedlemanWunch.matches_to_gapped_seqs() modifies arguments

[Tom Goddard]

I tried using NeedlemanWunch.matches_to_gapped_seqs(match_list, ...) to convert a match list to a pair of gapped sequences. Then I spent the next hour debugging because it reverses the match_list input argument. So the next time I call it with the same match_list list object all hell breaks lose giving an absurd pair of gapped sequences. The code should probably not modify its input arguments.