GenomicRanges intersect is more like what I would call set intersect - first the sets of A and B are computed, then intersection is done.

Bedtools intersect finds the intersect of each interval in A with each interval in B which means that in the worst case, the number of output regions is the size of the cartesian product of A B as in the example below:

$ cat A.bed
chr1  10  32
chr1  30  40

$ cat B.bed
chr1  15   35

$ bedtools intersect -a A.bed -b B.bed
chr1  15   32
chr1  30   35

Is this type of intersect possible in genomicranges? Thanks.

Edit: fixed example

See the HelloRanges package for this.