/** Pop the specified bubble if it is simple, otherwise scaffold. */
static void popOrScaffoldBubble(Graph& g, const Bubble& bubble)
{
#pragma omp atomic
g_count.bubbles++;
if (!popSimpleBubble(&g, bubble.front()) && opt::scaffold) {
#pragma omp atomic
g_count.scaffold++;
scaffoldBubble(g, bubble);
}
}
/** Scaffold over the bubble between vertices u and w.
* Add an edge (u,w) with the distance property set to the length of
* the largest branch of the bubble.
*/
static void scaffoldBubble(Graph& g, const Bubble& bubble)
{
typedef graph_traits<Graph>::vertex_descriptor V;
assert(opt::scaffold);
assert(bubble.size() > 2);
V u = bubble.front(), w = bubble.back();
if (edge(u, w, g).second) {
// Already scaffolded.
return;
}
assert(isBubble(g, bubble.begin(), bubble.end()));
assert(bubble.size() > 2);
size_t n = bubble.size() - 2;
g_popped.reserve(g_popped.size() + n);
for (Bubble::const_iterator it = bubble.begin() + 1;
it != bubble.end() - 1; ++it)
g_popped.push_back(it->contigIndex());
add_edge(u, w, max(longestPath(g, bubble), 1), g);
}
/** Return the length of the longest path through the bubble. */
static int longestPath(const Graph& g, const Bubble& topo)
{
typedef graph_traits<Graph>::edge_descriptor E;
typedef graph_traits<Graph>::out_edge_iterator Eit;
typedef graph_traits<Graph>::vertex_descriptor V;
EdgeWeightMap<Graph> weight(g);
map<ContigNode, int> distance;
distance[topo.front()] = 0;
for (Bubble::const_iterator it = topo.begin();
it != topo.end(); ++it) {
V u = *it;
Eit eit, elast;
for (tie(eit, elast) = out_edges(u, g); eit != elast; ++eit) {
E e = *eit;
V v = target(e, g);
distance[v] = max(distance[v], distance[u] + weight[e]);
}
}
V v = topo.back();
return distance[v] - g[v].length;
}
