search

OndrejSladky / kmercamel

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
MIT License
12 stars 2 forks source link

Different hashing for k-mers #64

Closed OndrejSladky closed 9 months ago

PavelVesely commented 9 months ago

@OndrejSladky did you run the tests and verification? Or should I do it?

OndrejSladky commented 9 months ago

@OndrejSladky did you run the tests and verification? Or should I do it?

The tests and verification are run automatically. I haven't tested the performance on the HG yet, so if that change of hash function to Wang hf didn't slow it down, we can merge it.

PavelVesely commented 9 months ago

The tests and verification are run automatically.

I see, that's great!

I haven't tested the performance on the HG yet, so if that change of hash function to Wang hf didn't slow it down, we can merge it.

Yes, on HG it's very fast, at least in the case that I used yesterday, that is, kmercamel optimize -c -k 19 -p 10_masked_superstrings/human.S_eulertigs.k_19.d_na.M_default.maskedSuperstring.txt -a zeros. It finished in 28 minutes, which is much less than the 40 minutes taken with the previous hash function.

So I'm merging this PR.