[BioC] Calculate Outer Positions of GappedAlignmentPairs

Dario Strbenac d.strbenac at garvan.org.au
Wed Mar 20 01:59:36 CET 2013


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.


Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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