Similar to how the coverage-function works with the weights argument, is there a way to use countOverlaps with weights? For example, using the score column of a bed file.

I currently do it via findOverlaps and then manipulating the Hits object, but this seems a bit slow and cumbersome - I feel like there's a GRanges trick I'm missing.

Here is a query and subject

query = GRanges(c("1:5-10", "1:7-12"))
subject = GRanges(c("1:6-6", "1:10-10"), score=10 * 1:2)

My implementation of your 'slow and cumbersome' is

hits = as(findOverlaps(query, subject), "List")
weightedCount = sum(extractList(subject$score, hits))

which I guess is a bit cumbersome but I think quite fast. In detail... us findOverlaps and coerce the return value to an IntegerList with one element for each query

> hits = as(findOverlaps(query, subject), "List")
> hits
IntegerList of length 2
[[1]] 1 2
[[2]] 2

Use extractList() to reformat the score column in a way that parallels the hits

> extractList(subject$score, hits)
NumericList of length 2
[[1]] 10 20
[[2]] 20

and finally use sum() to accumulate the score for each query element

> sum(extractList(subject$score, hits))
[1] 30 20