[Bioc-sig-seq] GRanges, failure assigning chromosome lengths

[Patrick Aboyoun]

Sean and Ivan,
Thanks for the insight. I'll look at devising a compromise within the 
existing framework. I need to explore the various methods for GRanges 
object to better understand the impact of a compromise. We started with 
the simplest interpretation of limit bounds because it simplifies the 
code. For example, we need to establish the rules for coverage or 
findOverlaps when the DNA is circular or the alignment runs off the end 
of a linear chromosome.


Patrick


On 4/27/10 8:05 AM, Sean Davis wrote:
> On Tue, Apr 27, 2010 at 10:51 AM, Ivan Gregoretti<ivangreg at gmail.com>  wrote:
>    
>> Good morning Sean and everybody,
>>
>>      
>>> Actually, the edge case is general as alignments, even on linear
>>> chromosomes, may extend beyond the end of the chromosome, I believe.
>>> In the best case, these alignments are clipped (in CIGAR terms), but I
>>> don't know that all aligners are doing that appropriately.
>>>
>>> Sean
>>>        
>> So, you rather go for an overriding switch rather than infrastructure overhaul?
>>
>> I ask this because GRanges is an exceptionally convenient format for
>> ChIP-seqers and Patrick is trying to make a decision to make it work
>> for real world data.
>>      
> I guess that I mean to say that the two issues of aligning off the end
> of the chromosome and handling circular genomes are related but
> separate issues.  An override seems quite reasonable for dealing with
> the former.  Until aligners or common formats (BAM/SAM) deal with the
> latter, it will be difficult to deal appropriately with circular
> genomes, so an override is probably a fine compromise.
>
> Sean
>
>
>    
>> And yes indeed: aligners do align a little bit past the boundaries
>> even for linear chromosomes. Thanks for pointing that out!
>>
>> Ivan
>>
>>