________________________________________
> De : David Eccles (gringer) [[email protected]]
> Date d'envoi : 1 juillet 2011 11:20
> À : [email protected]
> Objet : Re: [Denovoassembler-users] purpose of _getOutgoingEdges /
> _getIngoingEdges
>
> On 01/07/11 16:59, David Eccles (gringer) wrote:
>> I get that it's moving sequence around, and that 'ab' describes a 2-bit
>> location, rather than 2 base-pairs, but that's about the limit of my
>> guesses.
>
> Possibly some more insights from the Vertex code?
>
> /*
> * the vertex is important in the algorithm
> * a DNA sequence is simply an ordered array of vertices. Two consecutive
> * vertices always respect the de Bruijn property.
> * a Vertex actually stores two k-mers: only the lower is stored.
> * This halves the memory usage.
> */
>
> ...
>
> uint8_t m_edges_lower;
> uint8_t m_edges_higher;
>
> So, are the edges 8 bits (i.e. 4 bases) from each joining Kmer?
>
Yes, this idea is described in the ABySS paper.
1 bit per possible arc -- 4 in and 4 out.
> I've notice that these functions only seem to be used / callled in
> SeedWorker:
>
>
> $ grep -rl _getIngoingEdges *
> assembler/SeedWorker.cpp
> core/common_functions.h
> core/common_functions.cpp
> structures/Vertex.cpp
>
> So I presume it has something to do with finding / extending seeds???
>
Pretty much.
> -- David
>
Sébastien
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