kmers

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Discussion / possible features

2

Hi there! I'd like to discuss the state of this project to see if it would be suitable for larger Rust libraries. First I'd like to say that I really...

imartayan

Likely stupid question -> kmer u64 to kmer [u8]

8

I have created u64 representations of a kmer like this: ``` for kmer in needletail::kmer::Kmers::new(seq, 32 as u8 ) { let km = Kmer::from(kmer).into_u64(); ``` Is there a function to...

stela2502

Dealing with the (temporary) lack of constant computations in const generics

3

So, it turns out that currently (as of rust v1.51) with MVP const generics, we are not allowed to do simple computations with generic parameters. For example, it would be...

rob-p

Internal storage order

10

So after trying to write some code interfacing `kmers` with some k-mers parsed using `needletail`, I realized we are storing the k-mers in the opposite order. In `kmers` the leftmost...

rob-p

Encoding Type

7

I'm assuming we'd be using 2 bits per bp. There's a couple of common encodings, but I want to suggest ``` A -> 00 C -> 01 T -> 10...

Daniel-Liu-c0deb0t

Roadmap / TODO

3

This issue will provide a roadmap for the library, along with specific tasks (TODOs). Ideally we should break these tasks into short and long term tasks and, as the library...

rob-p

library name and logo?

6

As a fundamental start point for any good software project, we need to decide on the name and generate a logo. I kept the repo name simple, but I was...

rob-p

@rob-p A quick and dirty changeling logging differences to main. Notable changes: - QOL improvements to the naive kmer API (checked conversions, push_char) - Canonical minimizer iterators to emit minimizers...

theJasonFan