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 <[email protected]> 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 >>> >>> _______________________________________________ >>> [email protected] 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: [email protected] > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]]
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