[BioC] Performing set ops with an IRanges object loaded with elementMetadata is like a shotgun, pointing at my foot.

[Patrick Aboyoun]

Steve,
Most of the methods for the IRanges class predate the introduction of 
the elementMetadata slot and these methods have not been tested when the 
elementMetadata is not NULL. I have some changes I can check in to BioC 
2.7 to the gaps,IRanges-method and union,IRanges,IRanges-method that 
strips the elementMetadata from the output. Before I check it in, 
though, I want to survey all the methods to IRanges to see how many 
other methods need to be modified so I can make the change in one go, 
rather than in a piecemeal fashion. I'll let you know when my audit is 
complete and the modifications have been made.


Cheers,
Patrick




On 7/12/10 12:01 PM, Steve Lianoglou wrote:
> On Mon, Jul 12, 2010 at 2:49 PM, Michael Lawrence
> <lawrence.michael at gene.com>  wrote:
>    
>> On Mon, Jul 12, 2010 at 11:05 AM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com>  wrote:
>>      
> <snip>
>    
>>> I don't know what the answer *really* should be as to what the correct
>>> behavior in this situation would be, which I guess could be an
>>> interesting discussion ... perhaps the elementMetadata can be
>>> split/merged with its associated range, or just dropped all together
>>> (perhaps via some explicit parameter in the setdiff, etc. function
>>> call?).
>>>
>>> Anyway, in an effort to skirt that rabbit hole for now, could I ask
>>> for a feature request and have IRanges provide a more informative
>>> error message when an end user is gunning at their feet w/ this
>>> scenario? :-)
>>>
>>>        
>> I think it would be reasonable to simply drop the metadata, since one is
>> creating an entirely new set of ranges. Might want a warning/message, but
>> I'm not sure if even that is necessary. Just need to document the behavior.
>>      
> I agree that dropping the metadata is sufficient, but (if we were
> taking a vote) I think I'd have a slight (+0) preference for it to
> fire off a warning if any of the IRanges objects had metadata that was
> dropped.
>
>