complement

Description

Return intervals NOT covered by the input BED file. Reports gaps between intervals and uncovered chromosome regions.

Example Input

cat example_a.bed

chr1	100	200	gene1	100	+
chr1	150	250	gene2	200	-
chr1	400	500	gene3	300	+
chr2	100	300	gene4	400	+
chr2	500	700	gene5	500	-

cat genome.txt

chr1	1000
chr2	1000
chr3	1000

Command

grit complement -i example_a.bed -g genome.txt --assume-sorted

Output

chr1	0	100
chr1	250	400
chr1	500	1000
chr2	0	100
chr2	300	500
chr2	700	1000
chr3	0	1000

Options

Flag	Description
-i, --input	Input BED file
-g, --genome	Genome file (chrom sizes)
--assume-sorted	Assume input is sorted (enables O(1) memory streaming)

Notes

• Input must be sorted by chromosome and position
• Reports regions from genome file that have no coverage
• Chromosomes in genome file but not in input are fully reported
• Uses O(1) memory when --assume-sorted is specified