[BioC] bug report for GenomicRanges::findOverlaps

[Kasper Daniel Hansen]

GenomicRanges::findOverlaps does not support the same set of values
for 'select' and 'type' as the method for Ranges.  This is pretty easy
to fix, and seems to arise because the GenomicRanges version has the
usual
  function( ... type = c(...)) {
     type = match.arg(type)
  }
construction, but with type = c("any", "start", "end") instead of type
= c("any", "start", "end", "within", "equal").  A better long term fix
might be to not do the match.arg inside the method, but directly pass
the value of type and select into .findOverlaps.circle (which btw.
does exactly this: it simply passes the type and select arguments into
findOverlaps)

I am specifically interested in type = "within"

Kasper