On Sun, Feb 20, 2011 at 12:54 PM, Martin Morgan <[email protected]> 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 <[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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
