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? 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??? -- David ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
