<div dir="ltr"><div><div><div>Hi Titus,<br><br></div>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.<br><br></div>
I will try and see what happens.<br><br></div>Best,<br><br>Karl<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jul 29, 2013 at 5:18 PM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On Mon, Jul 29, 2013 at 02:28:34PM +0200, Karl Nordstr?m wrote:<br>
> Hi,<br>
><br>
> I would like to use khmer, but would like to keep the strand<br>
> information. After browsing the code and done some simple testing, as I<br>
> understand it, the common behaviour of khmer is to equal AAT with ATT. Is<br>
> this correct? and if so, is there a way around it?<br>
<br>
Hi Karl,<br>
<br>
yes, this is the default behavior. You can alter it by recompiling with<br>
NO_UNIQUE_RC set to 1 in lib/Makefile. However, we haven't thought deeply<br>
about the effect of this on diginorm or partitioning, so be careful! (Adding<br>
this functionality into khmer natively and testing it is something we are<br>
planning to do, but isn't in there yet.)<br>
<br>
If you correspond with us about what you want to do, we might be able to<br>
tell you when/if you'll have unpleasant or confounding effects of this<br>
change.<br>
<br>
Note, on ged-lab/bleeding-edge branch, 27 of the tests fail with NO_UNIQUE_RC<br>
set.<br>
<br>
cheers,<br>
--titus<br>
<span class="HOEnZb"><font color="#888888">--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu">ctb@msu.edu</a><br>
<br>
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