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

[Martin Morgan]

On 02/28/2010 11:51 AM, Martin Morgan wrote:
> On 02/28/2010 11:29 AM, Kasper Daniel Hansen wrote:
>> 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.
> 
> It's ironic in this circumstance, but a factor gives a controlled
> vocabulary -- no 'F' / 'R', for instance. Less compelling, representing
> a factor takes up less memory than a (vector of) character. Martin

I'll take the memory use back -- not only less compelling, but (nearly)
non-existent. Martin

> 
>>
>> 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
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> 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