calculate signature complexity

[taylorreiter]

would it be possible to combine size, scaled, and track-abundance info to calculate complexity of a signature in some way? I think what I want to know is the approx number of k-mers as a ratio of the input number of nucleotides

[ctb]

This strikes me as related to an issue that @luizirber proposed a while back - ISTR it was keeping track of abundance with HLL or some such. I can find it in the sourmash tracker, wonder if it's in khmer?

Anyway, a few thoughts --

• complexity is an overloaded term; it'd help to know your use cases for this feature?
• the specific question is straightforward to approximate but I'm not sure about approximation accuracy!
• the HULK paper might have some particular relevance to this!
• we might also want to look at the idea of computing more things as part of signatures (this is a bit out there) - as long as we're iterating over the data once, why not compute histosketches and other features?

Also see #246, tracking number of bp and input sequences.

[luizirber]

@ctb this? https://github.com/dib-lab/sourmash/pull/506

[ctb]

no... I'll chat about it in person!

[ctb]

ref https://github.com/sourmash-bio/sourmash/issues/33 too