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: [email protected]
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