wilcrofter / buzzhash Goto Github PK

Brilliant job, I have just seen this interesting paper, and find the open source code. I have seen your code, but it seems there isn't an example code. Can you give an example code? Thank you very much.

where do i find 'trainfeatures' ?

be nice to have some examples

I'm so glad this was done in Julia. I have significant experience writing Python, C++, etc. ,etc. but think it makes sense to transition to Julia for almost all of those use cases.

I'm just learning about rolling hashes and, as I understand, the benefit there is that you can re-use the already-calculated values between the ends, for the next window slide step. But maybe that savings is moot in cases like this, where a matrix multiplication on a precalculated binary lookup table is so cheap. IAW, it might be at least as fast as subtracting the last and adding the next step ends. IDK.

I just think the fly neural processing is cool and elegant, in and of itself, anyway. But I've been wondering if this has/can been/be adapted to genome mapping (aka alignment) to a reference. I wonder if it would be any faster (or more amenable to long nucleotide chains with 4 character alphabets) than minimap2
(GitHub repo)

"buzzmap", anyone? (taken)
"buzzgenmap"??