[Bioc-sig-seq] locally aligned reads

[Hans-Ulrich Klein]

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.

I would like to know whether someone has already implemented or intends 
to add some functionality for local alignments.

Best wishes,
Hans-Ulrich

-- 
Hans-Ulrich Klein
Department of Medical Informatics and Biomathematics
University of Münster
Domagkstrasse 9
48149 Münster, Germany
Tel.: +49 (0)251 83-58405