[Bioc-sig-seq] ShortRead + GappedAlignments -> QualityAlignedXStringSet?

Martin Morgan mtmorgan at fhcrc.org
Sun Feb 20 21:54:37 CET 2011

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

> 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 at 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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