closest

Description

Find the closest interval in B for each interval in A. Reports both overlapping and nearest non-overlapping intervals.

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 example_b.bed

chr1	120	180	feat1	50	+
chr1	220	280	feat2	60	-
chr1	450	480	feat3	70	+
chr2	150	250	feat4	80	+
chr2	600	650	feat5	90	-

Command

grit closest -a example_a.bed -b example_b.bed

Output

chr1	100	200	gene1	100	+	chr1	120	180	feat1	50	+
chr1	150	250	gene2	200	-	chr1	120	180	feat1	50	+
chr1	150	250	gene2	200	-	chr1	220	280	feat2	60	-
chr1	400	500	gene3	300	+	chr1	450	480	feat3	70	+
chr2	100	300	gene4	400	+	chr2	150	250	feat4	80	+
chr2	500	700	gene5	500	-	chr2	600	650	feat5	90	-

Options

Flag	Description
-a, --file-a	Input BED file A
-b, --file-b	Input BED file B
-d, --distance	Report distance in output
-t, --tie	Tie handling: all, first, last
--io	Ignore overlapping intervals
--iu	Ignore upstream intervals
--id	Ignore downstream intervals
-D, --max-distance	Maximum distance to report
--streaming	Use streaming mode (O(k) memory)
--assume-sorted	Skip sorted validation

Report Distance

grit closest -a example_a.bed -b example_b.bed -d

Ignore Overlaps

Find closest non-overlapping interval:

grit closest -a example_a.bed -b example_b.bed --io

Streaming Mode

grit closest -a example_a.bed -b example_b.bed --streaming --assume-sorted

Notes

• By default, reports all ties
• Use -t first or -t last to report only first/last tie
• Streaming mode requires sorted input