Question: NONCANONICAL flag

[FlyinTeller]

DSK is described to always work with canonical kmers. However, it seems that by adding -DNONCANONICAL=1 to the cmake call, one is able to change the behaviour of the underlying SortingCountAlgorithm:

#ifdef NONCANONICAL
    typedef typename Kmer<span>::template ModelMinimizer <ModelDirect>   Model;
#else
    typedef typename Kmer<span>::template ModelMinimizer <ModelCanonical>   Model;
#endif

It is documented for the GATB library, but I couldn't find a reference that doing this is intended to work with dsk. But as far as i can tell there shouldn't be anything from the code that prevents me from doing so? I am of ourse aware of the biological implications of doing this and also that the result will be about 2* as many kmers. I am mostly interested in if there is anything that should prevent dsk from working when switching to NONCANONICAL mode

[rchikhi]

Hi Flyin,
It works for DSK, as far as I know. But we really don't test that functionality that often, because well, all our applications are on canonical kmers. Best would be that you test it on a tiny dataset and see visually if it returns the expected result.
Rayan

[FlyinTeller]

Thank you for the quick answer. It worked fine on a toy example. When moving to real data I will do an extra evaluation if everything works as expected