[Bioc-sig-seq] locally aligned reads

[Patrick Aboyoun]

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.
>
> I would like to know whether someone has already implemented or 
> intends to add some functionality for local alignments.
>
> Best wishes,
> Hans-Ulrich
>