[BioC] IRanges coverage integer limit?

[Hervé Pagès]

Hi Nico,

The overflow issue is addressed in IRanges 1.15.18 (devel).

On 07/04/2012 02:16 AM, Nicolas Delhomme wrote:
> Great, thanks!
>
> Hervé - how much effort is it to extend it to numeric? I'm willing to do it, I just do not want to start on something where YOU would say it's though ;-)

I don't think it would be tough at all. The real question is: do we want
coverage() to always return a numeric-Rle instead of integer-Rle? This
will make the Rle 50% bigger in memory, probably not a big deal. On the
other hand this would allow treating numeric weights really as numerics
instead of truncating them like we do right now:

   > coverage(IRanges(1:3, width=10))
   'integer' Rle of length 12 with 5 runs
     Lengths: 1 1 8 1 1
     Values : 1 2 3 2 1
   > coverage(IRanges(1:3, width=10), weight=2.86)
   'integer' Rle of length 12 with 5 runs
     Lengths: 1 1 8 1 1
     Values : 2 4 6 4 2

Maybe one option would be to return an integer-Rle when 'weight' is
integer and a numeric-Rle when it's numeric. So by default (i.e. when
no weights are supplied) it would still return an integer-Rle (because
the default for 'weight' is 1L).
But coverage(IRanges(1:3, width=10), weight=2) would return a
numeric-Rle and coverage(IRanges(1:3, width=10), weight=2L)
an integer-Rle.

How does that sound?

H.

>
> Nico
>
> ---------------------------------------------------------------
> 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
> ---------------------------------------------------------------
>
>
>
>
>
> On Jul 3, 2012, at 8:00 PM, Hervé Pagès wrote:
>
>> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>>
>>
>>
>> --
>> 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 at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
>


-- 
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 at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319