[khmer] keep kmers stranded?

[Karl Nordström]

Hi Titus,

thank you very much. My intent was to write a simple filter with the help
of the data structures, not anything fancy. Learn how to make use of this
resource.

I will try and see what happens.

Best,

Karl


On Mon, Jul 29, 2013 at 5:18 PM, C. Titus Brown <ctb at msu.edu> wrote:

> On Mon, Jul 29, 2013 at 02:28:34PM +0200, Karl Nordstr?m wrote:
> > Hi,
> >
> > I would like to use khmer, but would like to keep the strand
> > information. After browsing the code and done some simple testing, as I
> > understand it, the common behaviour of khmer is to equal AAT with ATT. Is
> > this correct? and if so, is there a way around it?
>
> Hi Karl,
>
> yes, this is the default behavior.  You can alter it by recompiling with
> NO_UNIQUE_RC set to 1 in lib/Makefile.  However, we haven't thought deeply
> about the effect of this on diginorm or partitioning, so be careful!
>  (Adding
> this functionality into khmer natively and testing it is something we are
> planning to do, but isn't in there yet.)
>
> If you correspond with us about what you want to do, we might be able to
> tell you when/if you'll have unpleasant or confounding effects of this
> change.
>
> Note, on ged-lab/bleeding-edge branch, 27 of the tests fail with
> NO_UNIQUE_RC
> set.
>
> cheers,
> --titus
> --
> C. Titus Brown, ctb at msu.edu
>
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