<div dir="ltr">P.S. By 'python directory' in my last message I really meant the main khmer directory and the Makefile therein. Apologies for any confusion.<div class="gmail_extra"><br><br><div class="gmail_quote">
On Sun, Jun 16, 2013 at 1:09 AM, Lester Mackey <span dir="ltr"><<a href="mailto:lmackey@stanford.edu" target="_blank">lmackey@stanford.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Jordan,<div><br></div><div>If, after running 'make clean' in all directories, I set NO_UNIQUE_RC=1 in 'lib/Makefile' and then run 'make' in the higher level python directory, the Makefile fails to add -dNO_UNIQUE_RC=1 to CXXFLAGS when compiling the code in 'lib' (and so the reverse complement and kmer are still treated identically).</div>
<div><br></div><div>I've gotten around this by adding -dNO_UNIQUE_RC=1 to CXXFLAGS explicitly in python/Makefile, but I wanted to let you know in case this was not the desired behavior. </div><span class="HOEnZb"><font color="#888888"><div>
<br>
</div><div>Lester</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jun 14, 2013 at 5:53 AM, Jordan Fish <span dir="ltr"><<a href="mailto:jrdn.fish@gmail.com" target="_blank">jrdn.fish@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Lester,<div><br></div><div>Unless you are working with fairly small k-values you will probably want to use the CountingHash. Ktable handles simple exact counting so far large-ish values of k (>12, according to <a href="http://khmer.readthedocs.org/en/latest/ktable.html" target="_blank">http://khmer.readthedocs.org/en/latest/ktable.html</a>) it'll blow up.</div>
<div><br></div><div>The counting hash uses a bloom filter to limit memory usage at the cost of in-exact counting. Hopefully titus will jump in here with a link to some documentation on the inexact counting.</div><div><br>
</div><div>Finally, if you want to force khmer to treat a kmer and it's reverse complement as unique you will need to edit 'lib/Makefile' and change the line</div><div><br></div><div>NO_UNIQUE_RC=0</div><div>
<br>
</div><div>to</div><div><br></div><div>NO_UNIQUE_RC=1</div><div><br></div><div>and rebuild khmer<br><div class="gmail_extra"><br></div><div class="gmail_extra">Jordan<br><br><div class="gmail_quote"><div><div>
On Fri, Jun 14, 2013 at 3:22 AM, Lester Mackey <span dir="ltr"><<a href="mailto:lmackey@stanford.edu" target="_blank">lmackey@stanford.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Dear khmer Discussion List,<div><br></div>
<div>
If my goal is to obtain a vector of kmer counts quickly from a FASTA or FASTQ file, is there any reason to prefer ktable to one of your other data structures, like the counting hash table? </div></div></blockquote></div>
</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div>
<div dir="ltr">
<div><br></div><div>I've noticed that ktable hashes a kmer and its reverse complement to the same bin. Is there an easy way to disable this feature (and thereby count each kmer and reverse complement separately)?</div>
<div><br></div><div>Thanks,</div><div>Lester</div></div>
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