[BioC] bug report for GenomicRanges::findOverlaps

[Hervé Pagès]

Hi Kasper,

This is fixed in GenomicRanges 1.3.15 (devel).

Cheers,
H.


On 01/13/2011 11:17 PM, Hervé Pagès wrote:
> 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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