Just for the record, findOverlaps on GenomicRanges objects is
strand-specific.

In theory, insertion points could be internally represented with ranges
where end = start - 1. Then we could have a higher level class that makes
that more user friendly. Haven't had a use case yet, though.

Michael

On Wed, Jul 11, 2012 at 3:50 AM, Julien Gagneur <julien.gagneur@embl.de>wrote:

> Indeed, Nico.
>
> interval_overlap() can moreover be strand-specific (on
> Genome_intervals_stranded objects). It also deals with so-called
> "inter-base" positions, i.e positions between two nucleotides to represent,
> for example, insertion points or restriction enzyme cutting sites. One thus
> can ask whether cutting sites occurs within a set of exons without having
> to write extra code to deal with cutting sites right at exon boundaries.
>
> Best,
>
> Julien
>
> http://www.gagneur.genzentrum.lmu.de/
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