[BioC] narrow on GappedAlignments fails with error

[Hervé Pagès]

Hi Hubert, Martin,

This should be fixed in GenomicRanges 1.6.7 (release) and 1.7.24
(devel). Those new versions should become available thru biocLite() in
the next 24-36 hours. Please let me know if you still have problems
with this.

Thanks,
H.


On 01/20/2012 07:17 AM, Martin Morgan wrote:
> 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
>>
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>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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