EXP: skipmer sketching

[bluegenes]

Skipmers are something we've considered adding for quite some time, as DNA kmer that ~allows "mismatches".

Over in sourmash-bio/sourmash#3395, I added a Skipmer moltype and code in SeqToHashes to build skipmers. Here, I use that branch to sketch skipmers using the new buildutils. I think the rest of the branchwater functions should just work on skipmer sketches (but testing needed). Sourmash python functions cannot read or work with skipmer sigs.

There are two types of skipmers available, keep-2,skip-1 ("skipm2n3") and keep-1,skip-2 ("skipm1n3"). To sketch with skipmers, specify skipm2n3 or skipm1n3 in the parameter string. The skipmer ksize is the "final" size that the k-mer ends up. --i.e. for ksize 3, the sequence ACTAG would produce two skip-mers for m2n3: ACA, CTG.

example sketching commands:

manysketch:

sourmash scripts manysketch -p skipm2n3,k=21,scaled=100 ms.csv -o output.zip

singlesketch:

sourmash scripts singlesketch -p skipm2n3,k=21,scaled=100 myfile.fasta -o myfile.sig.gz

-o myfile.zip also works