merge

Description

Merge overlapping or adjacent intervals into single intervals. Uses streaming algorithm with O(1) memory.

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	-

Command

grit merge -i example_a.bed --assume-sorted

Output

chr1	100	250
chr1	400	500
chr2	100	300
chr2	500	700

Options

Flag	Description
-i, --input	Input BED file (use - for stdin)
-d, --distance	Maximum distance between intervals to merge (default: 0)
-s, --strand	Require strand to match for merging
-c, --count	Report count of merged intervals
--in-memory	Use in-memory mode (handles unsorted input)
--assume-sorted	Skip sorted validation
--stats	Print streaming statistics to stderr

Merge with Distance

Merge intervals within 100bp of each other:

grit merge -i example_a.bed -d 100 --assume-sorted

Count Merged Intervals

grit merge -i example_a.bed -c --assume-sorted

Output:

chr1	100	250	2
chr1	400	500	1
chr2	100	300	1
chr2	500	700	1

Strand-Specific Merge

grit merge -i example_a.bed -s --assume-sorted

Notes

• Input must be sorted by chromosome and position
• Use --assume-sorted for pre-sorted input to skip validation
• Uses O(1) memory in streaming mode