Handling of columns with gaps

tseemann / snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

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Handling of columns with gaps #29

Open kloetzl opened 5 years ago

kloetzl commented 5 years ago

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 commented 5 years ago

Normally I would advise running

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

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

kloetzl commented 5 years ago

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? :wink: