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

Aaron Taudt aaron.taudt at gmail.com
Thu Mar 17 09:10:51 CET 2016

Hi Peter,

GenomicAlignments::readGAlignmentPairs() can take a while to
(correctly) fail if the `which` parameter contains a "bad" seqlevel.
It'd be great if it failed early in the following scenario (just

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 (


	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list