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

[Kasper Daniel Hansen]

Would it not make sense to return a character vector instead of a
factor?  As we see, factors tends to bit you, and there is no
particular reason for having a factor in this particular example.

Kasper

On Sun, Feb 28, 2010 at 2:03 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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
>
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