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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
