It would make sense for this to be granges,GappedAlignmentPairs. Want to
contribute it?

Michael


On Tue, Mar 19, 2013 at 5:59 PM, Dario Strbenac <d.strbenac@garvan.org.au>wrote:

> Hello,
>
> I would like to calculate the furthest outer positions of the mapped read
> pairs. That is, the lowest and highest mapped coordinate of a read. In a
> later step, I want to get a coverage estimate that also includes coverage
> of the spliced out intron parts. I couldn't find any function already in
> GenomicRanges. I made my own code to create a GRanges object of these
> simple ranges, but was curious about any API functionality I overlooked
> that could do this.
>
> Thanks,
>            Dario.
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
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