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