option to control comparisons to missing bases

tseemann / snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

GNU General Public License v3.0

126 stars 28 forks source link

option to control comparisons to missing bases #17

Closed SionBayliss closed 6 years ago

SionBayliss commented 6 years ago

Useful!

Could there be an option to change the how comparisons of ATCG to missing bases (N/-/? etc) are handled by snp-dists? It would be useful to have the choice of calculating distances between all sites or just sites containing ATCG.

tseemann commented 6 years ago

Yes, I am implementing now, will be in 0.5

tseemann commented 6 years ago

@SionBayliss now, by default, it will only count AGTC vs AGTC If you want the old behaviour, use the -a (all chars) option. I am also added a -k (keep case) option to remove AGTC vs agtc problems.