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

[Aaron Taudt]

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
experienced).

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

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