Handling of columns with gaps

[kloetzl]

Currently, snp-dists only cares about gaps in pairwise comparison. However, common alignment tools such as MEGA have a complete deletion mode where the whole column is ignored if any of the sequences contains a gap there. Adding a switch for this might be of interest.

[tseemann]

Normally I would advise running

snp-sites -c file.aln | snp-dists /dev/stdin

for that case, but it's still worth considering.

[kloetzl]

it's still worth considering.

You can just add it to the wishlist.

snp-sites -c file.aln | snp-dists /dev/stdin

Hm, I would expect to use - to read from stdin, maybe even nothing at all. Should I create another PR? 😉