[BioC] IRanges coverage integer limit?

[Hervé Pagès]

On 07/03/2012 09:40 AM, Nicolas Delhomme wrote:
> Hi,
>
> I've just discovered that the IRanges coverage function would "overflow" without warnings. Below is an example that reproduce it:
>
> library(IRanges)
> rngs <- IRanges(c(1:100),width=100)
> coverage(rngs)
>
> 'integer' Rle of length 199 with 199 runs
>    Lengths:  1  1  1  1  1  1  1  1  1  1  1 ...  1  1  1  1  1  1  1  1  1  1
>    Values :  1  2  3  4  5  6  7  8  9 10 11 ... 10  9  8  7  6  5  4  3  2  1
>
> coverage(rngs,weight=1e9)
>
> 'integer' Rle of length 200 with 200 runs
>    Lengths:           1           1           1 ...           1           1
>    Values :  1000000000  2000000000 -1294967296 ...  1000000000           0
>
> runValue(coverage(rngs,weight=1e9))
>    [1]  1000000000  2000000000 -1294967296  -294967296   705032704  1705032704
>    [7] -1589934592  -589934592   410065408  1410065408 -1884901888  -884901888
> ...
>
> Clearly, the third position that has a coverage of 3 (not weighted) has a 3e9 weighted one which is > 2^31 (signed integer limit on most machine). I'm just surprised that it is silently ignored.
>
> For NGS, getting a bp coverage > 2^31 is unlikely, although I've already seen extremely high coverage for Ribosomal-like protein that were only 10 order of magnitude away (~2M X). This limits the ranges of weights that can be used (weight as of now can only be integers), i.e. a weight of 100 would already be borderline.
>
> Is there a way around this, coverage being such a very handy function? I understand that weight being integers probably makes computation faster, but what could be the overhead of allowing numeric instead? And I don't mind looking under the hood if that helps.

Thanks Nico for catching this other one. I will keep operations in the
int space for now (so an 'integer' Rle is always returned) but will make
sure a warning is issued and NAs are returned in case of overflow.

H.

>
> Cheers,
>
> Nico
>
> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] IRanges_1.15.17    BiocGenerics_0.3.0
>
> loaded via a namespace (and not attached):
> [1] stats4_2.15.1 tools_2.15.1
>
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
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-- 
Hervé Pagès

Program in Computational Biology
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