[BioC] narrow on GappedAlignments fails with error

[Martin Morgan]

On 01/20/2012 05:14 AM, Hubert Rehrauer wrote:
> Hi
>
> There seems to be an overvflow problem if the GappedAlignments object
> holds many reads:

Yes that looks like a bug; it will take some time to be fixed. Thanks. 
Martin

>
> With foo being a gapped alignments having 17836148 reads I get:
>> bar = narrow( foo[1:10000000], di[1:10000000]) ## fine
>> bar = narrow( foo[10000000:17836148], di[10000000:17836148]) ## fine
>> bar = narrow( foo, di)
>> Error during wrapup: in 'cigar' element 11380048: CIGAR is empty after
>> narrowing
>> Warning messages:
>> 1: In successiveIRanges(cigarToWidth(cigar)) :
>> Integer overflow in 'cumsum'; use 'cumsum(as.numeric(.))'
>> 2: In start(x) + width(x) : NAs produced by integer overflow
>> 3: In start(x) + width(x) : NAs produced by integer overflow
>> 4: In start(x) + width(x) : NAs produced by integer overflow
> can you help???
>
> hubert
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793