[BioC] countOverlaps within Mode Counting

Dario Strbenac D.Strbenac at garvan.org.au
Thu Mar 1 23:00:15 CET 2012


Yes, the question was how many reads fall totally inside each gene. Your example shows what I was trying to do, but I was trying to do it in one line with countOverlaps, which doesn't seem possible with the current semantics of the Within mode, since it groups by the query ranges, but the query ranges have to be inside the subject ranges. It's quite simple, as you show, to do it by summarizing the overlap result, so I suppose it's not needed.

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