Bioconductor / GenomicRanges

Representation and manipulation of genomic intervals
https://bioconductor.org/packages/GenomicRanges
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Sorting a SortedByQueryHits produces a Hits #2

Closed LTLA closed 6 years ago

LTLA commented 6 years ago

Running the following code on the current GenomicRanges devel version (1.31.3):

library(GenomicRanges)
example(GenomicRanges, echo=FALSE)
olap <- findOverlaps(gr, gr)
class(sort(olap))

... gives a Hits object, while previously in the release (1.30.0) it gave a SortedByQueryHits object. Is this change intentional? I am curious because my InteractionSet package defines its own findOverlaps method, and I would like to know what the correct return class should be.

lawremi commented 6 years ago

Sorry, my bad, I fixed this in S4Vectors