sshash-lib

Core library for SSHash-rs: a compressed k-mer dictionary based on sparse and skew hashing.

Quick Start

use sshash_lib::{Dictionary, Kmer, KmerBits};

type Kmer31 = Kmer<31>;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    // Load a previously built index
    let dict = Dictionary::load("index")?;

    // Single k-mer lookup (returns position or INVALID_UINT64)
    let kmer = Kmer31::from_string("ACGTACGTACGTACGTACGTACGTACGTACG")?;
    let pos = dict.lookup::<31>(&kmer);

    // Streaming queries over a sequence
    let mut engine = dict.create_streaming_query::<31>();

    Ok(())
}

Modules

License

MIT