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

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