manysketch: check ambiguous nucleotide handling

[bluegenes]

To be consistent with sourmash functionality, we should ignore k-mers with N's.
I initially used force to avoid throwing out records with N's, but I wanted to double check whether the behavior is as expected.

Digging in to see if I understand what is happening:

relevant branchwater manysketch code:

https://github.com/sourmash-bio/sourmash_plugin_branchwater/blob/main/src/manysketch.rs#L234-L236

 if moltype == "protein" {
     sig.add_protein(&record.seq())
     .expect("Failed to add protein");
} else {
    // if not force, panics with 'N' in dna sequence
    sig.add_sequence(&record.seq(), true)
    .expect("Failed to add sequence");

Relevant sourmash core code: https://github.com/sourmash-bio/sourmash/blob/0af3cbb828e77676496abd1dfe0196818c54c511/src/core/src/signature.rs#L38C5-L58C6

fn add_sequence(&mut self, seq: &[u8], force: bool) -> Result<(), Error> {
        let ready_hashes = SeqToHashes::new(
            seq,
            self.ksize(),
            force,
            false,
            self.hash_function(),
            self.seed(),
        );

        for hash_value in ready_hashes {
            match hash_value {
                Ok(0) => continue,
                Ok(x) => self.add_hash(x),
                Err(err) => return Err(err),
            }
        }

        // Should be always ok
        Ok(())
    }

Without force, I think add_sequence returns an Error if any of the k-mers have an N, meaning we lose the entire record, rather than just k-mers with N's?

in SeqToHashes: https://github.com/sourmash-bio/sourmash/blob/0af3cbb828e77676496abd1dfe0196818c54c511/src/core/src/signature.rs#L274-L282

 if !VALID[self.sequence[j] as usize] {
    if !self.force {
       return Some(Err(Error::InvalidDNA {
            message: String::from_utf8(kmer.to_vec()).unwrap(),
       }));
    } else {
       self.kmer_index += 1;
       // Move the iterator to the next step
       return Some(Ok(0));

So force allows us to push past invalid k-mers, which I think is the right behavior!

ref: sourmash-bio/sourmash#137, https://github.com/sourmash-bio/sourmash/pull/138/files

cc @ctb in case you have thoughts