grit subtract

Remove intervals in A that overlap with B.

Usage

grit subtract [OPTIONS] -a <FILE_A> -b <FILE_B>

Options

Option	Description
-a, --file-a <FILE>	Input BED file A
-b, --file-b <FILE>	Input BED file B
-A, --remove-entire	Remove entire A feature if any overlap
-f, --fraction <F>	Minimum overlap fraction required
-r, --reciprocal	Require reciprocal fraction overlap
--streaming	Use streaming mode (O(k) memory)
--assume-sorted	Skip sorted validation
--allow-unsorted	Allow unsorted input
-g, --genome <FILE>	Genome file for chromosome order validation

Examples

Basic subtraction

# Remove overlapping portions
grit subtract -a regions.bed -b blacklist.bed > clean.bed

# Streaming mode for large files
grit subtract -a regions.bed -b blacklist.bed --streaming --assume-sorted

Remove entire intervals

# Remove entire A interval if ANY overlap with B
grit subtract -a genes.bed -b repeats.bed -A > non_repeat_genes.bed

Minimum overlap fraction

# Only subtract if overlap is at least 50%
grit subtract -a regions.bed -b mask.bed -f 0.5 > filtered.bed

Output

Input A:

chr1    100    300
chr1    400    500

Input B:

chr1    150    200

Output (default):

chr1    100    150
chr1    200    300
chr1    400    500

Output (with -A):

chr1    400    500

Visual Example

A:      |------------|        |------|
B:           |--|

Result: |----| |----|        |------|
        ^kept^ ^kept^        ^kept^
             ^removed^

Performance

# Fastest for sorted input
grit subtract -a sorted_a.bed -b sorted_b.bed --streaming --assume-sorted

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