<div dir="ltr"><div>Dear Jordan,</div><div><br></div>Does the counting hash have a built-in way to enumerate used hash table entries without having to iterate over every hash table entry?<div><br></div><div>On a slightly related note, if I have 16GB of memory to work with, is it advisable to choose hash_size = min(4**k, 16e9)/4 and n_tables = 4 when calling new_counting_hash for k-mer counting?</div>
<div><br></div><div>Thanks,</div><div>Lester<br><div class="gmail_extra"><br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
<div>
> ><br>
> > On Fri, Jun 14, 2013 at 3:22 AM, Lester Mackey <<a href="mailto:lmackey@stanford.edu" target="_blank">lmackey@stanford.edu</a>>wrote:<br>
> ><br>
> >> Dear khmer Discussion List,<br>
> >><br>
> >> If my goal is to obtain a vector of kmer counts quickly from a FASTA or<br>
> >> FASTQ file, is there any reason to prefer ktable to one of your other data<br>
> >> structures, like the counting hash table?<br>
> >><br>
> ><br>
> >> I've noticed that ktable hashes a kmer and its reverse complement to the<br>
> >> same bin. Is there an easy way to disable this feature (and thereby count<br>
> >> each kmer and reverse complement separately)?<br>
> >><br>
> >> Thanks,<br>
> >> Lester<br>
> >><br>
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> >><br>
> >><br>
> ><br>
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<br>
<br>
</div></div><div><div>--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
</div></div></blockquote></div><br></div></div><span></span></div>