[Bioc-sig-seq] readAligned and BAM format

[Wu Wei]

Hi Martin,

I am also looking for that. Would you please also forward that  
additional info to me.

Thanks,
Wave

On 2 Nov 2009, at 14:34, Martin Morgan wrote:

> 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
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
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Wu Wei
Postdoctoral Fellow
Steinmetz Group, EMBL Heidelberg
Tex: +49 6221 387-8310 (8114)
Fax: +49 6221 387-8518
Email: wuwei at embl.de