[Bioc-devel] Making GenomicAlignments::readGAlignmentPairs() fail fast if given bad seqlevels in `which`

Peter Hickey peter.hickey at gmail.com
Thu Mar 17 15:29:23 CET 2016

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]]

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