On Sun, Feb 20, 2011 at 12:54 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 02/20/2011 06:47 AM, Michael Lawrence wrote:
> > 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.
>
> A class would be good, yes. Perhaps the cigar is sufficient for
> describing indels, with sequence / quality information as
> elementMetadata on the GappedAlignments object plus functions in
> ?"cigar-utils" enough to get consensusMatrix, etc.? Martin
>
>
There's definitely a good amount of functionality surrounding cigar strings
and aligned sequences. It just seems like it's one step away.

Michael


> > 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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> >
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>
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