rust-lapper

Documentation

Crates.io

This is a rust port of Brent Pendersen's nim-lapper. It has a few notable differences, mostly that the find and seek methods both return iterators, so all adaptor methods may be used normally.

Example

use rust_lapper::{Interval, Lapper};

type Iv = Interval<u32>;
fn main() {
    // create some fake data
    let data: Vec<Iv> = vec![
        Iv{start: 70, stop: 120, val: 0}, // max_len = 50
        Iv{start: 10, stop: 15, val: 0},
        Iv{start: 10, stop: 15, val: 0}, // exact overlap
        Iv{start: 12, stop: 15, val: 0}, // inner overlap
        Iv{start: 14, stop: 16, val: 0}, // overlap end
        Iv{start: 40, stop: 45, val: 0},
        Iv{start: 50, stop: 55, val: 0},
        Iv{start: 60, stop: 65, val: 0},
        Iv{start: 68, stop: 71, val: 0}, // overlap start
        Iv{start: 70, stop: 75, val: 0},
    ];

    // Make lapper structure
    let mut lapper = Lapper::new(data);
    
    // Iterator based find to extract all intervals that overlap 6..7
    // If your queries are coming in start sorted order, use the seek method to retain a cursor for
    // a big speedup.
    assert_eq!(
        lapper.find(11, 15).collect::<Vec<&Iv>>(), vec![
            &Iv{start: 10, stop: 15, val: 0},
            &Iv{start: 10, stop: 15, val: 0}, // exact overlap
            &Iv{start: 12, stop: 15, val: 0}, // inner overlap
            &Iv{start: 14, stop: 16, val: 0}, // overlap end
        ]
    );

    // Merge overlapping regions within the lapper to simlify and speed up queries that only depend
    // on 'any' overlap and not how many
    lapper.merge_overlaps();
    assert_eq!(
        lapper.find(11, 15).collect::<Vec<&Iv>>(), vec![
            &Iv{start: 10, stop: 16, val: 0},
        ]
    );

    // Get the number of positions covered by the lapper tree:
    assert_eq!(lapper.cov(), 73);

    // Get the union and intersect of two different lapper trees
    let data = vec![
        Iv{start: 5, stop: 15, val: 0},
        Iv{start: 48, stop: 80, val: 0},
    ];
    let (union, intersect) = lapper.union_and_intersect(&Lapper::new(data));
    assert_eq!(union, 88);
    assert_eq!(intersect, 27);
}