https://github.com/harryscholes/kmer-minhash

A library for parallel k-mer min-wise hashing
https://github.com/harryscholes/kmer-minhash

Last synced: 3 months ago
JSON representation

A library for parallel k-mer min-wise hashing

• Host: GitHub
• URL: https://github.com/harryscholes/kmer-minhash
• Owner: harryscholes
• Created: 2021-11-11T21:14:59.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2023-01-08T17:12:51.000Z (over 2 years ago)
• Last Synced: 2025-02-05T10:49:12.707Z (4 months ago)
• Language: Rust
• Homepage:
• Size: 14.6 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# kmer-minhash

Parallel _k_-mer min-wise hashing in Rust.

This package provides:

- `Kmers` struct for representing the _k_-mers of some sequence

- `KmersIntoIter` struct for iterating over the _k_-mers

- `MinHash` trait for min-wise hashing of _k_-mers

### Example

```rust

use std::collections::hash_map::DefaultHasher;

use std::hash::{Hash, Hasher};

use kmer_minhash::{Kmers, MinHash};

const KMER_SIZE: usize = 3;

const N_HASHES: usize = 2;

fn main() {

    let seq = "abcde";

    let kmers = Kmers::from_str(seq, KMER_SIZE);

    let min_hashes = kmers.min_hash(N_HASHES).unwrap();

    // Check that the minhashes are correct:

    let mut manual_hashes = vec!["abc", "bcd", "cde"]

        .iter()

        .map(|kmer| {

            let mut hasher = DefaultHasher::new();

            kmer.hash(&mut hasher);

            hasher.finish()

        })

        .collect::>();

    manual_hashes.sort();

    assert_eq!(min_hashes, manual_hashes[..N_HASHES]);

}

```

See the tests in `src/lib.rs` for more examples of how to use this package with Rayon and Tokio.