| 10 | */ |
| 11 | template <typename Graph> |
| 12 | size_t loadKmer(Graph& g, FastaReader& in) |
| 13 | { |
| 14 | typedef typename graph_traits<Graph>::vertex_descriptor V; |
| 15 | |
| 16 | assert(opt::rank == -1); |
| 17 | size_t count = 0; |
| 18 | for (FastaRecord rec; in >> rec;) { |
| 19 | assert(rec.seq.size() == V::length()); |
| 20 | std::istringstream iss(rec.id); |
| 21 | float coverage = 1; |
| 22 | iss >> coverage; |
| 23 | assert(iss); |
| 24 | assert(iss.eof()); |
| 25 | g.add(V(rec.seq), std::max(1, (int)ceilf(coverage))); |
| 26 | |
| 27 | if (++count % 1000000 == 0) { |
| 28 | logger(1) << "Read " << count << " k-mer. "; |
| 29 | g.printLoad(); |
| 30 | } |
| 31 | g.pumpNetwork(); |
| 32 | } |
| 33 | assert(in.eof()); |
| 34 | return count; |
| 35 | } |
| 36 | |
| 37 | template <typename Graph> |
| 38 | bool loadSequence(Graph* seqCollection, Sequence& seq) |
no test coverage detected