Compute table of hamming distances between all sequences

[torognes]

Computing the all-vs-all hamming distances between sequences in a set would be a useful feature, even if it is not very fast.

[torognes]

I've added the --distance option which will write the distance between the sequences to the pairs file when computing overlaps. This is usually the Hamming distance (minimum number of substitutions), unless the --indel (or `-i´) option is specified, in which case the distance is the Levenshtein distance (minimum number of substitutions or indels).

I hope this could serve a similar purpose.