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#ifndef ASSEMBLY_ADJACENCYALGORITHM_H
#define ASSEMBLY_ADJACENCYALGORITHM_H 1
namespace AssemblyAlgorithms {
/** Generate the adjacency information for each sequence in the
* collection. */
template <typename Graph>
size_t generateAdjacency(Graph* seqCollection)
{
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename Graph::Symbol Symbol;
typedef typename Graph::SymbolSet SymbolSet;
Timer timer("GenerateAdjacency");
size_t count = 0;
size_t numBasesSet = 0;
for (typename Graph::iterator iter = seqCollection->begin();
iter != seqCollection->end(); ++iter) {
if (iter->second.deleted())
continue;
if (++count % 1000000 == 0)
logger(1) << "Finding adjacent k-mer: " << count << '\n';
for (extDirection dir = SENSE; dir <= ANTISENSE; ++dir) {
V testSeq(iter->first);
Symbol adjBase = testSeq.shift(dir);
for (unsigned i = 0; i < SymbolSet::NUM; ++i) {
testSeq.setLastBase(dir, Symbol(i));
if (seqCollection->setBaseExtension(
testSeq, !dir, adjBase))
numBasesSet++;
}
}
seqCollection->pumpNetwork();
}
if (numBasesSet > 0) {
logger(0) << "Added " << numBasesSet << " edges.\n";
if (!opt::db.empty())
addToDb("EdgesGenerated", numBasesSet);
}
return numBasesSet;
}
} // namespace AssemblyAlgorithms
#endif
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