Hi,

I may have missed something but,

I have 2 ranges objects like this:

suppressPackageStartupMessages(library(GenomicRanges))
#> Warning: package 'S4Vectors' was built under R version 3.5.1

rg1 = GenomicRanges::GRanges(seqnames = c(1,1,2),
                             IRanges(start = c(1,10,1),
                                     end = c(9,19,20))
                             )
rg1
#> GRanges object with 3 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]        1       1-9      *
#>   [2]        1     10-19      *
#>   [3]        2      1-20      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths

rg2 = GenomicRanges::GRanges(seqnames = c(1),
                             IRanges(start = c(5),
                                     end = c(15))
)

rg2
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]        1      5-15      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

Then I want to intesect them by maintaining the adjacent intances in the original rg1 into different instances in the result object

The default behaviour merge them in the same instance:

rg_intersect = GenomicRanges::intersect(rg1,rg2)

rg_intersect
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]        1      5-15      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths

I tried to merge after applying a findOverlaps method, because the result of the FO method only gives 2 hits so I would expect that it also gives 2 instances. However, it also merges the 2 things.

findOverlapPairs(rg1,rg2)
#> Pairs object with 2 pairs and 0 metadata columns:
#>           first    second
#>       <GRanges> <GRanges>
#>   [1]     1:1-9    1:5-15
#>   [2]   1:10-19    1:5-15

GenomicRanges::intersect(findOverlapPairs(rg1,rg2))
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]        1      5-15      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths

Created on 2019-03-25 by the reprex package (v0.2.0).