Re: [Seqan-dev] countKmers
Hi Stephen,
currently there is not much of a difference between the trunk and the 1.4 release, which we tagged from the trunk just a couple of days ago. In the release we simply merged the trunk folders core/include and extras/include into one include folder.
You'll get the countKmers functions if you include the alignment_free module by #include <seqan/alignment_free.h>. You can find the sources in (extras/)include/seqan/alignment_free/kmer_functions.h
HTH,
David
--
David Weese weese@inf.fu-berlin.de
Freie Universität Berlin http://www.inf.fu-berlin.de/
Institut für Informatik Phone: +49 30 838 75137
Takustraße 9 Algorithmic Bioinformatics
14195 Berlin Room 020
Am 09.05.2013 um 13:31 schrieb "Henderson, Stephen" <s.henderson@ucl.ac.uk>:
> Hello
>
> I think I'm confused by what is the current/trunk/development versions? I have downloaded 1.4 which I think is the trunk? I had to change a few keywords (Mapped -> StringReader) to make my old code work. But I do not see the useful countKmers function that I downloaded the latest version for:
>
> countKmers(kmerCounts, sequence, k)
> countKmers(kmerCounts, backgroundFrequencies, sequence, k)
> countKmers(kmerCounts, bgModel, sequence, k)
>
> This should be in align_free and align_free.h ?
>
> Is this in a dev version somewhere?
>
> Thanks
> Stephen Henderson
> UCL Cancer Institute
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