[khmer] Unique reverse-complement

[C. Titus Brown]

great, thanks for following through!

On Thu, Dec 08, 2016 at 01:16:07PM +0000, Bintu, Bogdan wrote:
> Dear Titus,
> 
> Great. This solved it.
> 
> Thanks,
> 
> Bogdan
> 
> From: C. Titus Brown<mailto:ctbrown at ucdavis.edu>
> Sent: Wednesday, December 7, 2016 8:33 PM
> To: Bintu, Bogdan<mailto:bbintu at fas.harvard.edu>
> Cc: khmer at lists.idyll.org<mailto:khmer at lists.idyll.org>
> Subject: Re: [khmer] Unique reverse-complement
> 
> 
> 
> Hi Bogdan,
> 
> apparently we changed things in some of our Makefile refactoring -- since
> we don't test this regularly, it went unnoticed!
> 
> A "proper" fix will have to wait, but for now you can modify lib/kmer_hash.hh
> like so:
> 
> % diff --git a/lib/kmer_hash.hh b/lib/kmer_hash.hh
> ----
> index 1c6c86f..5b4f5d3 100644
> --- a/lib/kmer_hash.hh
> +++ b/lib/kmer_hash.hh
> @@ -87,11 +87,7 @@ Contact: khmer-project at idyll.org
>  #endif
> 
>  // choose wisely between forward and rev comp.
> -#ifndef NO_UNIQUE_RC
> -#define uniqify_rc(f, r) ((f) < (r) ? (f) : (r))
> -#else
>  #define uniqify_rc(f,r)(f)
> -#endif
> 
> 
>  namespace khmer
> ---
> 
> That is, remove the #ifndef, first #define, #else, and #endif from that
> file so it just says 'uniqify_rc(f,r)(f)'.
> 
> You'll be happy to know that soonish we may have a supported way to do
> this at runtime rather than compole time!
> 
> --titus
> 
> On Thu, Dec 08, 2016 at 12:51:04AM +0000, Bintu, Bogdan wrote:
> > P.S.
> > I originally started with the indications in the link:
> > http://lists.idyll.org/pipermail/khmer/2013-June/000394.html
> > Another person was trying to achieve the same thing as I am and had similar issues. He managed to solve the problem
> >
> > ?by adding -dNO_UNIQUE_RC=1 to CXXFLAGS explicitly?
> > in the Makefile in the root khmer folder.
> > I did not figure out where exactly to add this. I also do not know whether this person?s reported bug was fixed in later versions.
> > Regards,
> > Bogdan
> >
> >
> > From: Bintu, Bogdan<mailto:bbintu at fas.harvard.edu>
> > Sent: Wednesday, December 7, 2016 4:21 PM
> > To: C. Titus Brown<mailto:ctbrown at ucdavis.edu>
> > Cc: khmer at lists.idyll.org<mailto:khmer at lists.idyll.org>
> > Subject: RE: [khmer] Unique reverse-complement
> >
> >
> > Dear Titus,
> >
> > Thanks for the prompt reply.
> >
> > Tried what you suggested but sadly it did not solve it.
> >
> > Any other suggestion?
> >
> > Regards,
> >
> > Bogdan
> >
> >
> >
> > From: C. Titus Brown<mailto:ctbrown at ucdavis.edu>
> > Sent: Wednesday, December 7, 2016 3:32 PM
> > To: Bintu, Bogdan<mailto:bbintu at fas.harvard.edu>
> > Cc: khmer at lists.idyll.org<mailto:khmer at lists.idyll.org>
> > Subject: Re: [khmer] Unique reverse-complement
> >
> >
> >
> > On Wed, Dec 07, 2016 at 08:18:31PM +0000, Bintu, Bogdan wrote:
> > > Dear Dr. Brown,
> > >
> > > I am a graduate student using your khmer package.
> > > I am trying to construct a khmer.Countgraph which is not degenerate between a sequence and its reverse complement.
> > > More explicitly, in python when running:
> > >
> > > import Khmer
> > > ht = khmer.Countgraph(17,10,1)
> > > ht.consume('GGCTTGCTCCAGCCATG')
> > > ht.get('CATGGCTGGAGCAAGCC')
> > >
> > > I would like the last line to return 0.
> > >
> > > As suggested in a different thread I tired modifying NO_UNIQUE_RC=0 to NO_UNIQUE_RC=1 in lib/Makefile and then run python setup.py install.
> > > But this did not solve my issue.
> > >
> > > Any help would be appreciated.
> >
> > Hi Bogdan,
> >
> > thanks for the email!
> >
> > Can you try doing:
> >
> > make clean
> > python setup.py install
> >
> > after the modification?  That should work.
> >
> > thanks,
> > --titus
> > --
> > C. Titus Brown, ctbrown at ucdavis.edu
> 
> --
> C. Titus Brown, ctbrown at ucdavis.edu

-- 
C. Titus Brown, ctbrown at ucdavis.edu