Hi everybody I want to load bam-files from different sources into GappedAlignments, but don't know which tags are actually available in the bam-File. With scanBam this is no problem, if the tag was not in the bam it just puts NULL in that place. The readGappedAlignments method however fails. Now the question: Is there a method to find out which tags are actually present in a bam-file????? regards, hubert

On 11/18/2011 06:51 AM, Hubert Rehrauer wrote: > Hi everybody > > I want to load bam-files from different sources into GappedAlignments, > but don't know which tags are actually available in the bam-File. > > With scanBam this is no problem, if the tag was not in the bam it just > puts NULL in that place. The readGappedAlignments method however fails. If I understand correctly, > example(scanBam) > readBamGappedAlignments(fl,param=ScanBamParam(tag="FO")) Error in rep.int(NA, count) : incorrect type for second argument which is probably a bug and will be fixed. > > Now the question: Is there a method to find out which tags are actually > present in a bam-file????? I don't think so; the bam file would have to be parsed for this. Could be a feature to be added... Martin > > regards, > 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