[Bioc-devel] mapToAlignments_issue

[David Porubsky]

Dear Bioc-team,

I'm trying to map genome coordinates back to local (contig/read)
coordinates, however, I have an issue to do this properly in cases when
alignment between contig and the genome (reference) is in minus (reverse)
orientation.
Is there a way to use function GenomicAlignments::mapToAlignments in strand
aware fashion such that reverse alignments will be mapped in minus
orientation?

Is there an example code on how to this properly?

Thank you in advance,

David

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