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 <[email protected]> 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 >> >> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
