On 02/12/2010 06:28 AM, Patrick Aboyoun wrote: > Hans-Ulrich, > We at the Hutch are currently adding support for alignments with indels > (I/D/S) and gaps (N) to Rsamtools in time for the BioC 2.6 release. What > functionality would you consider to be a must have for the BioC 2.6 > release? We don't have a full spec for the release and your input, and > that of others, would be of great value to us. > > > Patrick > > On 2/12/10 2:38 AM, Hans-Ulrich Klein wrote: >> Dear All, >> >> I am working with reads that have local alignments. That means, that >> the reads only partially align to the reference. A read may also have >> two or more subsequences that align to different positions. The BioC >> class AlignedRead is not suitable in this situation. Also the >> Rsamtools package does not support reads that have e.g. "D", "I" or >> "S" within their cigar strings.
For what it's worth, Rsamtools scanBam does currently input these reads; the cigar is a factor and interpretable by the end user; as Patrick says things are in the works for much richer support. Martin >> >> I would like to know whether someone has already implemented or >> intends to add some functionality for local alignments. >> >> Best wishes, >> Hans-Ulrich >> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
