[khmer] keep kmers stranded?

[C. Titus Brown]

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