Overlappers (Wasm)

Wasm binding for gtars-overlaprs: a low-level interval overlap engine. Build an Overlapper once from a set of reference regions (the "universe"), then ask which of those regions each query region overlaps. For whole-region-set operations (intersections, unions, statistics), use RegionSet instead.

Import

import init, { Overlapper } from '@databio/gtars';

await init();

Construction

const universe = [
  ['chr1', 100, 200, 'a'],
  ['chr1', 150, 250, 'b'],
  ['chr2', 300, 400, 'c'],
];

const overlapper = new Overlapper(universe, 'ailist');

• universe: an array of [chr, start, end, name] entries. The binding reads each entry as a four-element tuple, so include a name (any string; it is not used).
• backend: the index to build for each chromosome, either 'ailist' (augmented interval list) or 'bits' (binary interval search). Any other value throws Invalid backend specified.

Methods

get_backend()

Returns the backend name the overlapper was built with ('ailist' or 'bits').

find(regions)

Takes an array of query regions in the same [chr, start, end, name] form and returns one flat array of the universe regions they overlap, each as [chr, start, end]. Overlaps from all queries are concatenated in query order, so a universe region that overlaps two queries appears twice. Queries on a chromosome that is not in the universe contribute nothing.

const hits = overlapper.find([['chr1', 180, 220, 'q1']]);
// [['chr1', 100, 200], ['chr1', 150, 250]]