[BioC] bug report for GenomicRanges::findOverlaps

[Hervé Pagès]

Hi Kasper,

Thanks for the report. I'll take care of this and will come back
here when it's done.

H.

On 01/13/2011 09:09 AM, Kasper Daniel Hansen wrote:
> 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
>
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-- 
Hervé Pagès

Program in Computational Biology
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