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<p class="x_MsoNormal">Dear Titus,</p>
<p class="x_MsoNormal">Great. This solved it.</p>
<p class="x_MsoNormal">Thanks,</p>
<p class="x_MsoNormal">Bogdan</p>
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<p class="x_MsoNormal" style="border:none; padding:0in"><b>From: </b><a href="mailto:ctbrown@ucdavis.edu">C. Titus Brown</a><br>
<b>Sent: </b>Wednesday, December 7, 2016 8:33 PM<br>
<b>To: </b><a href="mailto:bbintu@fas.harvard.edu">Bintu, Bogdan</a><br>
<b>Cc: </b><a href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br>
<b>Subject: </b>Re: [khmer] Unique reverse-complement</p>
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<div class="PlainText">Hi Bogdan,<br>
<br>
apparently we changed things in some of our Makefile refactoring -- since<br>
we don't test this regularly, it went unnoticed!<br>
<br>
A "proper" fix will have to wait, but for now you can modify lib/kmer_hash.hh<br>
like so:<br>
<br>
% diff --git a/lib/kmer_hash.hh b/lib/kmer_hash.hh<br>
----<br>
index 1c6c86f..5b4f5d3 100644<br>
--- a/lib/kmer_hash.hh<br>
+++ b/lib/kmer_hash.hh<br>
@@ -87,11 +87,7 @@ Contact: khmer-project@idyll.org<br>
#endif<br>
<br>
// choose wisely between forward and rev comp.<br>
-#ifndef NO_UNIQUE_RC<br>
-#define uniqify_rc(f, r) ((f) < (r) ? (f) : (r))<br>
-#else<br>
#define uniqify_rc(f,r)(f)<br>
-#endif<br>
<br>
<br>
namespace khmer<br>
---<br>
<br>
That is, remove the #ifndef, first #define, #else, and #endif from that<br>
file so it just says 'uniqify_rc(f,r)(f)'.<br>
<br>
You'll be happy to know that soonish we may have a supported way to do<br>
this at runtime rather than compole time!<br>
<br>
--titus<br>
<br>
On Thu, Dec 08, 2016 at 12:51:04AM +0000, Bintu, Bogdan wrote:<br>
> P.S.<br>
> I originally started with the indications in the link:<br>
> <a href="http://lists.idyll.org/pipermail/khmer/2013-June/000394.html">http://lists.idyll.org/pipermail/khmer/2013-June/000394.html</a><br>
> Another person was trying to achieve the same thing as I am and had similar issues. He managed to solve the problem<br>
> <br>
> ?by adding -dNO_UNIQUE_RC=1 to CXXFLAGS explicitly?<br>
> in the Makefile in the root khmer folder.<br>
> 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.<br>
> Regards,<br>
> Bogdan<br>
> <br>
> <br>
> From: Bintu, Bogdan<<a href="mailto:bbintu@fas.harvard.edu">mailto:bbintu@fas.harvard.edu</a>><br>
> Sent: Wednesday, December 7, 2016 4:21 PM<br>
> To: C. Titus Brown<<a href="mailto:ctbrown@ucdavis.edu">mailto:ctbrown@ucdavis.edu</a>><br>
> Cc: khmer@lists.idyll.org<mailto:khmer@lists.idyll.org><br>
> Subject: RE: [khmer] Unique reverse-complement<br>
> <br>
> <br>
> Dear Titus,<br>
> <br>
> Thanks for the prompt reply.<br>
> <br>
> Tried what you suggested but sadly it did not solve it.<br>
> <br>
> Any other suggestion?<br>
> <br>
> Regards,<br>
> <br>
> Bogdan<br>
> <br>
> <br>
> <br>
> From: C. Titus Brown<<a href="mailto:ctbrown@ucdavis.edu">mailto:ctbrown@ucdavis.edu</a>><br>
> Sent: Wednesday, December 7, 2016 3:32 PM<br>
> To: Bintu, Bogdan<<a href="mailto:bbintu@fas.harvard.edu">mailto:bbintu@fas.harvard.edu</a>><br>
> Cc: khmer@lists.idyll.org<mailto:khmer@lists.idyll.org><br>
> Subject: Re: [khmer] Unique reverse-complement<br>
> <br>
> <br>
> <br>
> On Wed, Dec 07, 2016 at 08:18:31PM +0000, Bintu, Bogdan wrote:<br>
> > Dear Dr. Brown,<br>
> ><br>
> > I am a graduate student using your khmer package.<br>
> > I am trying to construct a khmer.Countgraph which is not degenerate between a sequence and its reverse complement.<br>
> > More explicitly, in python when running:<br>
> ><br>
> > import Khmer<br>
> > ht = khmer.Countgraph(17,10,1)<br>
> > ht.consume('GGCTTGCTCCAGCCATG')<br>
> > ht.get('CATGGCTGGAGCAAGCC')<br>
> ><br>
> > I would like the last line to return 0.<br>
> ><br>
> > 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.<br>
> > But this did not solve my issue.<br>
> ><br>
> > Any help would be appreciated.<br>
> <br>
> Hi Bogdan,<br>
> <br>
> thanks for the email!<br>
> <br>
> Can you try doing:<br>
> <br>
> make clean<br>
> python setup.py install<br>
> <br>
> after the modification? That should work.<br>
> <br>
> thanks,<br>
> --titus<br>
> --<br>
> C. Titus Brown, ctbrown@ucdavis.edu<br>
<br>
-- <br>
C. Titus Brown, ctbrown@ucdavis.edu<br>
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