Add option to ignore reads containing "N" (unknown/any nucleotide)

[boulund]

Is it possible to add an option to ignore reads containing "N" (unknown/any nucleotide)? I know I should probably remove those reads, but maybe it could be useful anyway?

[betatim]

If you run sourmash with the -f option it will skip kmers that contain a character that isn't one of ACGT. Does that work for you?

[boulund]

Sounds great. I misunderstood what the --force option would do from the help text. You can close this if you want to.

[betatim]

Which sub-command did you look at? I just looked at sourmash compute -h which doesn't say anything about what -f does. I'll keep this open as a reminder to fix that.

[boulund]

Actually never looked at the command line help from the version I was using (oops). I was reading along in the documentation (https://sourmash.readthedocs.io/en/latest/command-line.html)

--force -- recompute existing signatures; convert non-DNA characters to N

[betatim]

Actually, sorry I confused force and force ... what you are looking for is --check-sequence

[betatim]

#172 fixes the lack of documentation

[ctb]

Closed by #240.