[Bioc-sig-seq] readAligned and BAM format

[Martin Morgan]

Joern Toedling wrote:
> Hi everyone,
> 
> has anybody by chance already written a parser for importing alignments in
> BAM/SAM format into objects of class AlignedRead? This format seems to be
> gaining more and more support, yet it is still absent from the options in
> function readAligned. If one of you already has written such a parsing
> function and would not mind sharing it, please let me know.

Hi Joern -- there is a package in the Bioc svn repository that does
this; it is not yet in the devel branch, there are some limitations in
terms of AlignedRead (e.g., AlignedRead currently supports only ungapped
alignments, whereas BAM allows gapped). I'll forward additional info
off-list.

Martin
> 
> Best regards,
> Joern
> 
> ---
> Joern Toedling
> Institut Curie -- U900
> 26 rue d'Ulm, 75005 Paris, FRANCE
> Tel. +33 (0)156246926
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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