Right now, AlignedRead only contains the position for a mapped read and
leaves off any indel information. GappedAlignments has this. Would it be
possible to combine GappedAlignments and a QualityScaledXStringSet (i.e.,
from a ShortRead object) to get a QualityAlignedXStringSet? It would be nice
to merge the sequence-based alignment infrastructure in Biostrings with the
range-based alignment representation in GenomicRanges.

Thoughts?

Michael

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