Hi Martin thanks for the clarification, yes it works. Sorry my fault. And there are unmapped reads in the file. The bam holds paired-end alignments from the LifeScope software. If only one of the reads in a pair gets mapped Lifescope still reports both, and obviously one of them has the unmapped flag. regards, hubert On 05.07.12 19:31, Martin Morgan wrote: > Hi Hubert -- > > On 07/05/2012 11:33 AM, Hubert Rehrauer wrote: >> Dear developers >> >> In the following case countBam does not give the expected result: >> >>> param = ScanBamParam() > > this creates bamWhat(param) == character(), which is to say 'don't > read anything in', and explains why scanBam returns a 0-length named > list. > >>> bamFlag(param) = scanBamFlag(isUnmappedQuery=TRUE) > > It's also possible to create this as > > ScanBamParam(flag=scanBamFlag(isUnmappedQuery=TRUE)) > > though probably you want > > ScanBamParam(flag=scanBamFlag(isUnmappedQuery=TRUE), > what="qname") > >>> cb = countBam(bamFile, param=param) >>> cb >> space start end width file records nucleotides >> 1 NA NA NA NA 4541.bam 3157955 133205755 >>> bamReads = scanBam(bamFile, param=param)[[1]]$qname >>> scanBam(bamFile, param=param)[[1]] >> named list() >> >> >> There are no unmapped reads in my bamFile and so it should return 0, >> or am I wrong? > > So maybe there are unmapped reads (if setting what="qname" returns > something)? > > example(scanBamFlag) > > and then exploring the bam file pointed to by 'fl' seem to suggest > that the flag is being interpreted correctly. If you're not convince, > it would help to have sessionInfo() and bamFile, and if possible a > small sample (use ?filterBam?) of your bam file? > > Martin > >> >> regards, >> hubert >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > >