[Bioc-sig-seq] strand() in ShortRead, Rsamtools

[Martin Morgan]

Hi all --

I want to be a bit more explicit about a user-visible change that might
cause some confusion. This has to do with the development version of
ShortRead, and the unreleased version of Rsamtools.

Previously, strand() returned levels c("-", "+", "*"). This changed in
BSgenome 1.15.10 svn revsion 44085 (2010-01-19). ShortRead didn't catch
up to this revision until today (version 1.5.18, revision 44930);
Rsamtools caught up in version 0.1.34. Rsamtools also made an important
change in the way reads on the reverse strand are handled, see
news(package="Rsamtools").

Martin
-- 
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