Thanks, Aaron. I implemented a similar workaround, but I think it would be nice to have in the core Bioconductor implementation. I had a quick poke around GenomicAlignments::readGAlignmentPairs(), however, but it looked like I'd have to learn a bit too much about the underlying Rsamtools::scanBam() in order to implement a quick fix.
> > Hi Peter, > > I had the same problem a while ago and solved it by first reading only the > header of the BAM file, extracting the chromosomes that are available and > generating a warning for all given chromosomes that are not available. That > worked for my purposes. I have implemented this in a function ( > https://github.com/ataudt/aneufinder/blob/master/R/importReads.R) > > Aaron > > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
