Hi,

The GappedAlignments class is very useful, since we do not have to load the
sequence information from a BAM file. I might suggest that GappedAlignments
gain a Seqinfo slot (or an element in the metadata), which would be e.g.
derived from the BAM header. That way, we get the right info on
GRanges(List)s derived from the object and the coverage method can use the
lengths. It would also be nice if AlignedRead could hold such information
for when we care about the sequence.

Thanks,
Michael

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