[BioC] narrow on GappedAlignments fails with error

[Hubert Rehrauer]

Hi

There seems to be an overvflow problem if the GappedAlignments object 
holds many reads:

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