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.

This crate works well for most interval data that does not include very long intervals that engulf a majority of other intervals. It is still fairly comparable to other methods. If you absolutely need time guarantees in the worst case, see COItres and IITree.

However, on more typical datasets, this crate is between 4-10x faster than other interval overlap methods.

It should also be noted that the count method is agnostic to data type, and should be about as fast as it is possible to be on any dataset. It is an implementation of the BITS algorithm

Serde Support

rust-lapper supports serialization with serde for Lapper and Interval objects:

toml [dependencies] rust-lapper = { version = "*", features = ["with_serde"] }

See examples/serde.rs for a brief example.

Benchmarks

Benchmarking interval tree-ish datastructures is hard Please see the interval_bakeoff project for details on how the benchmarks were run... It's not fully baked yet though, and is finiky to run.

Command to run:

``` ./target/release/interval_bakeoff fake -a -l RustLapper -l RustBio -l NestedInterval -n50000 -u100000

This equates to the following params:

num_intervals 50000

universe_size 100000

minintervalsize 500

maxintervalsize 80000

addlargespan true (universe spanning)

```

Set A / b Creation Times

| crate/method | A time | B time | | ---------------- | -------- | -------- | | rustlapper | 15.625ms | 31.25ms | | nestedintervals | 15.625ms | 15.625ms | | bio | 15.625ms | 31.25ms |

100% hit rate (A vs A)

| crate/method | mean time | intersection | | ---------------------------------- | ---------- | ------------ | | rustlapper/find | 4.78125s | 1469068763 | | rustlapper/count | 15.625ms | 1469068763 | | nestedintervals/queryoverlapping | 157.4375s | 1469068763 | | bio/find | 33.296875s | 1469068763 |

Sub 100% hit rate (A vs B)

| crate/method | mean time | intersection | | ---------------------------------- | ---------- | ------------ | | rustlapper/find | 531.25ms | 176488436 | | rustlapper/count | 15.625ms | 176488436 | | nestedintervals/queryoverlapping | 11.109375s | 196090092 | | bio/find | 4.3125s | 176488436 |

nested_intervals rust-bio Note that rust-bio has a new interval tree structure which should be faster than what is shown here

Example

```rust use rust_lapper::{Interval, Lapper};

type Iv = Interval; fn main() { // create some fake data let data: Vec = 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 overlaping regions within the lapper to simplifiy and speed up quries that only depend
// on 'any
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);

// Get the depth at each position covered by the lapper
for interval in lapper.depth().filter(|x| x.val > 2) {
    println!(
        "Depth at {} - {}: {}",
        interval.start, interval.stop, interval.val
    );
}

} ```

Release Notes

-0.4.0: Addition of the BITS count algorithm. -0.4.2: Bugfix in to update starts/stops vectors when overlaps merged -0.4.3: Remove leftover print statement -0.5.0: Make Interval start/stop generic -1.0.0: Add serde support via the with_serde feature flag