Is integer.max dependent on 32bit vs 64bit?  It seems to me that the OP
specifically complains that he cannot represent 995*10^6 as an integer.
 Also, is there a sign issue here as well?


On Tue, Dec 3, 2013 at 2:53 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi,
>
> Agreed with Martin that until someone comes up with a chromosome that
> is longer than .Machine$integer.max I don't see the need for switching
> to double or int64 to represent the seqlengths.
>
> Furthermore, since the seqlengths are used in many range operations
> like checking the validity of the ranges in a GRanges object, trimming
> them, computing coverage, handling circularity, etc... it would not
> make much sense to make the switch for the seqlengths without also
> making it for Ranges objects. That would be a serious undertaking though
> and probably with many backward compatibility issues.
>
> H.
>
>
>
> On 12/03/2013 10:07 AM, Martin Morgan wrote:
>
>> On 12/03/2013 02:29 AM, Julian Gehring wrote:
>>
>>> Hi,
>>>
>>> Some of the chromosomes out in the world are fairly large (e.g. wheat
>>> chr 3B
>>> with > 995 Mbp [1]).  Currently, the 'seqlengths' of the reference
>>> sequence are
>>> stored as 'integers' which do not allow to store lengths of this
>>> size.  Are
>>> there any plans of switching to 'doubles' or 64-bit integers for the
>>> 'seqlengths' slot?  Or extending the slot such that a user can store
>>> it either
>>> as integer or floating-point number?
>>>
>>
>> But
>>
>>  > .Machine$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
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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