Disjoining Intervals

This section covers patterns for splitting intervals at breakpoints using GIQL’s DISJOIN operator – partitioning a set into non-overlapping segments and re-tiling features against a reference grid.

Partition a Set of Intervals

Build a Disjoint Partition

Split a set of intervals into the maximal set of non-overlapping sub-intervals defined by its own breakpoints:

SELECT DISTINCT disjoin_chrom, disjoin_start, disjoin_end
FROM DISJOIN(features)
ORDER BY disjoin_chrom, disjoin_start

Use case: Given ChIP-seq peak calls pooled from several samples, produce a non-overlapping segment track – the equivalent of Bioconductor’s disjoin() – so downstream signal or count aggregates never double-count a base covered by two overlapping sample peaks.

Track Each Segment’s Parent

Keep the parent feature alongside each sub-interval:

SELECT name, disjoin_start, disjoin_end
FROM DISJOIN(features)
ORDER BY name, disjoin_start

Use case: See how each original feature was fragmented and which segment came from which parent.

Split Against a Reference

Split Features Against a Mask

Cut target features at the boundaries of a reference (mask) set, keeping only the pieces the mask covers:

SELECT name, disjoin_start, disjoin_end
FROM DISJOIN(features, reference := mask)

Use case: Restrict ATAC-seq or gene features to a set of callable (or otherwise interesting) mask regions, splitting them at the mask boundaries so no reported piece straddles a mask edge.

Re-tile Against a Uniform Grid

Pass a generated set of fixed-width bins as the reference:

WITH bins AS (
    SELECT 'chr1' AS chrom, x AS start, x + 1000 AS "end"
    FROM range(0, 250000000, 1000) AS t(x)
)
SELECT * FROM DISJOIN(features, reference := bins)

Use case: Break features onto a uniform coordinate grid – for example to build a fixed-width binned coverage matrix – so each piece falls within a single bin.

Note

range() is DuckDB-specific syntax for generating the bin grid; other engines need their own generator. The grid must also span every chromosome present in features, or features on an uncovered chromosome are dropped.

Coming from Bedtools?

DISJOIN has no direct bedtools equivalent – no single bedtools command splits intervals at breakpoints. See the Bedtools Migration Guide guide for the GIQL operators that do map onto bedtools commands.