Implement skani as fastani alternative

[AroneyS]

Add skani as fastani alternative

• Refactor fastani implementation to allow enumeration
  • Assert threshold > 1 (in new method?)
  • Move find_representatives and find_memberships back into clusterer.rs
  • Pass Clusterer through above functions so it needs only implement calculate_ani
  • Need get_threshold method?
• Add skani as fastani alternative
  • Implement calculate_skani
• Add to cli

[wwood]

Yeh I think that's roughly the idea

[AroneyS]

Higher than for fastani. Skani gives ANI of >98% for all pairs measured.

[AroneyS]

Few steps closer. Still need to add to cli.
Also may be faster to let skani handle the fileio in bulk, like in https://github.com/bluenote-1577/skani-lib-example/blob/main/src/main.rs. But then we would need independent logic for skani/fastani, since it would calculate all pairs up-front. Could add it to the initialise method for skani and then reference a look-up table in calculate_ani...

[wwood]

Are you thinking per-disconnected component after the preclusterer? Or just in total? If the latter then no point in preclustering, I think.

[AroneyS]

Not sure. Both are possibilities, though skani doesn't recommend comparing genomes with <82% ANI, so we would have to deal with that if we skip preclustering, right? Though it says "If the resulting aligned fraction for the two genomes is < 15%, no output is given.", so maybe <82% just doesn't give an answer, rather than giving an unreliable answer.

[AroneyS]

This is getting a bit unwieldy. I tried a let preclusterer = match, but it doesn't work since they are different types. Should the Preclusterer/Clusterer enum's be defined using the underlying structs instead of dummy ones?

[wwood]

So the issue is that here we have to define the behaviour for every combination of clusterer and preclusterer, right?

I think the answer is yes, well enum or dyn, up to you

[AroneyS]

Also, I get this warning on compile: warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4, partitions v0.2.4

[AroneyS]

--cluster-method isn't in the --full-help. Is there somewhere that I missed? Or do I have to rebuild docs?

[wwood]

I didn't go through every line, but seems about good. I think you need to add skani to the conda yml, and can you enable runs on PR using

on: [push, pull_request]

in the actions yml please?

[wwood]

--cluster-method isn't in the --full-help. Is there somewhere that I missed? Or do I have to rebuild docs?

You added that argument, so won't show up until docs are redployed from main/release.