[Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric

Martin Morgan mtmorgan at fhcrc.org
Tue Dec 3 19:07:21 CET 2013

On 12/03/2013 02:29 AM, Julian Gehring wrote:
> Hi,
> Some of the chromosomes out in the world are fairly large (e.g. wheat chr 3B
> with > 995 Mbp [1]).  Currently, the 'seqlengths' of the reference sequence are
> stored as 'integers' which do not allow to store lengths of this size.  Are
> there any plans of switching to 'doubles' or 64-bit integers for the
> 'seqlengths' slot?  Or extending the slot such that a user can store it either
> as integer or floating-point number?


 > .Machine$integer.max
[1] 2147483647

so we at least survive wheat chr 3B?

If there is movement to support this I'd encourage exact representation as 
double (this is how R deals with long vectors, and I believe it is the 
javascript representation of integers so not completely unprecedented) rather 
than 64 bit integers (which do not have any support in R).

I guess this would be quite a big undertaking so real use cases need to be 
present. And support for larger integers would seem to be useful to R generally 
rather than just to Bioc.


> Best wishes
> Julian
> [1] http://www.sciencemag.org/content/322/5898/101
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