Struct QueryMerFile 

pub struct QueryMerFile { /* private fields */ }

Random-access query interface for Jellyfish binary/sorted database files.

Uses memory-mapped I/O and matrix-guided binary search for efficient k-mer lookups, matching the behavior of Jellyfish’s C++ binary_query class.

Examples

use jellyfish_reader::{QueryMerFile, MerDna};

let qf = QueryMerFile::open("output.jf").unwrap();
let mer: MerDna = "ACGTACGTACGTACGTACGTACGTA".parse().unwrap();
match qf.get(&mer) {
    Some(count) => println!("{} appears {} times", mer, count),
    None => println!("{} not found", mer),
}

Implementations

impl QueryMerFile

pub fn open<P: AsRef<Path>>(path: P) -> Result<Self>

Open a Jellyfish database file for random-access queries.

pub fn get(&self, mer: &MerDna) -> Option<u64>

Look up the count for a k-mer. Returns None if not found.

pub fn query(&self, kmer_str: &str) -> Result<Option<u64>>

Query a k-mer given as a string. Convenience method.

pub fn header(&self) -> &FileHeader

Get the file header.

pub fn k(&self) -> usize

K-mer length (number of bases).

pub fn num_records(&self) -> usize

Number of records in the file.