Hi, Yes, that works fine, thanks. It must've been a size issue I was having.
---- Original message ---- >Date: Mon, 13 Dec 2010 17:31:24 +1000 >From: Paul Leo <[email protected]> >Subject: Re: [Bioc-sig-seq] scanBam Error >To: [email protected] >Cc: [email protected] > > Do you need all the sequence data at once? > > Instead of using a smaller bam file can you read in > a smaller portion of your large bamfile ? > > data.gr<-GRanges(seqnames > =paste("chr",13,sep=""),ranges = > IRanges(start=as.numeric(28608234),end=as.numeric(28608363)),strand="+") > > which<- data.gr > > params<-ScanBamParam(which=which,flag=scanBamFlag(isUnmappedQuery=FALSE,isDuplicate=NA,isValidVendorRead=TRUE),simpleCigar > = FALSE,reverseComplement = > > FALSE,what=c("qname","flag","rname","seq","strand","pos","mpos","qwidth","cigar","qual","mapq","isize", > "mrnm" ),tag="RG" ) # change to what you want > aln1 <- scanBam("HS1808.bam",param=params) > > aln1[[1]] > > That should work fine? > >-- >Dr Paul Leo >Bioinformatician >UQ Diamantina Institute for Cancer, Immunology and Metabolic Medicine >--------------------------------------------------------------------- >Level 4, R Wing >Princess Alexandra Hospital >Ipswich Rd >Woolloongabba QLD 4102 >Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 >Email: [email protected] Web: http://www.di.uq.edu.au > > -----Original Message----- > From: Dario Strbenac <[email protected]> > Reply-to: [email protected] > To: [email protected] > Subject: Re: [Bioc-sig-seq] scanBam Error > Date: Mon, 13 Dec 2010 17:15:38 +1100 > > I tried it out by making a smaller bam file with only reads from one > chromosome, and it worked fine. The full bam file is 4 GB and has 75 million > reads in it. Could the size be a problem ? Could you test out a bam file of > this size on your end, without me sending you one that big ? Also, the error > is different after I put the scamBamParam in the right spot : > > Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) : > negative length vectors are not allowed > > Integer overflow somewhere, maybe ? > > - Dario. > > ---- Original message ---- > >Date: Sun, 12 Dec 2010 20:59:23 -0800 > >From: Martin Morgan <[email protected]> > >Subject: Re: [Bioc-sig-seq] scanBam Error > >To: [email protected] > >Cc: [email protected] > > > >On 12/12/2010 08:00 PM, Dario Strbenac wrote: > >> Hello, > >> > > > >> I'm having trouble reading in a BAM file when "seq" is one of the > >strings passed to the what argument of ScanBamParam. If it's not, then > >the the reading completes successfully. I don't understand what the > >error means. It is : > >> > >> Error in .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = > >> param) : > >> INTEGER() can only be applied to a 'integer', not a 'closure' > >> > >> The traceback is : > >> > >>> traceback() > >> 4: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) > >> 3: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) > >> 2: scanBam("HS1808.bam", flag = ScanBamFlag(isDuplicate = FALSE), > >> param = ScanBamParam(reverseComplement = TRUE, what = c("rname", > >> "strand", "pos", "seq"))) > >> 1: scanBam("HS1808.bam", flag = ScanBamFlag(isDuplicate = FALSE), > >> param = ScanBamParam(reverseComplement = TRUE, what = c("rname", > >> "strand", "pos", "seq"))) > >> > >> and the environment is : > >> > >> R version 2.12.0 (2010-10-15) > >> Platform: x86_64-pc-mingw32/x64 (64-bit) > >> > >> locale: > >> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 > >> LC_MONETARY=English_Australia.1252 LC_NUMERIC=C > >> LC_TIME=English_Australia.1252 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] Rsamtools_1.2.1 Biostrings_2.18.0 GenomicRanges_1.2.0 > >> IRanges_1.8.2 > >> > >> loaded via a namespace (and not attached): > >> [1] Biobase_2.8.0 > > > >Hi Dario -- this is some kind of error in Rsamtools' C code, but I'm not > >able to reproduce it on my end so can't track it down. Is there any way > >of producing and sharing with me an example file that has this problem? > > > >One thing (not causing the bug) in your traceback is that 'flag' should > >be an argument to ScanBamParam; as it is I think it is being silently > >ignored. > > > >Martin > > > >> > >> -------------------------------------- > >> Dario Strbenac > >> Research Assistant > >> Cancer Epigenetics > >> Garvan Institute of Medical Research > >> Darlinghurst NSW 2010 > >> Australia > >> > >> _______________________________________________ > >> Bioc-sig-sequencing mailing list > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > > >-- > >Computational Biology > >Fred Hutchinson Cancer Research Center > >1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > > >Location: M1-B861 > >Telephone: 206 667-2793 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
