Hi all,

In assigning RNA-seq data to exon-models, I'm looking for a proper overlap
function. Both IRanges and genomeIntervals have overlap functions, but as
far as I can see, these don't have options for contained overlaps, example:


|-------Range 1-------]
     [----Range 2----]

IRanges, genomeIntervals: TRUE
Wanted: TRUE


|-------Range 1-------]
                 [----Range 2----]


IRanges, genomeIntervals: TRUE
Wanted: FALSE

Any suggestions are appreciated!

Regards,
Johannes Waage,
Uni. of Copenhagen

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