Looked into this a little and found that QualityAlignedXStringSet can only
represent insertions or deletions, not both. To represent both, you would
need two such objects, one for the read, one for the reference. Something
like a PairwiseAlignedFixedSubject, but without all the pairwise alignment
stuff.

Anyway, such a thing would be nice to have. For example, consensusMatrix
would give us a pileup.

Michael

On Sun, Feb 20, 2011 at 6:32 AM, Michael Lawrence <michafla@gene.com> wrote:

> 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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