/** Assemble overlapping paths. */
static void assembleOverlappingPaths(Graph& g,
Paths& paths, vector<string>& pathIDs)
{
if (paths.empty())
return;
// Find overlapping paths.
Overlaps overlaps = findOverlaps(g, paths);
addPathOverlapEdges(g, paths, pathIDs, overlaps);
// Create a property map of path overlaps.
OverlapMap overlapMap;
for (Overlaps::const_iterator it = overlaps.begin();
it != overlaps.end(); ++it)
overlapMap.insert(OverlapMap::value_type(
OverlapMap::key_type(
it->source.descriptor(),
it->target.descriptor()),
it->overlap));
// Assemble unambiguously overlapping paths.
Paths merges;
assemble_if(g, back_inserter(merges),
IsPathOverlap(g, overlapMap, IsPositive<Graph>(g)));
// Merge overlapping paths.
g_contigNames.unlock();
assert(!pathIDs.empty());
setNextContigName(pathIDs.back());
for (Paths::const_iterator it = merges.begin();
it != merges.end(); ++it) {
string name = createContigName();
if (opt::verbose > 0)
cerr << name << '\t' << *it << '\n';
Vertex u(paths.size(), false);
put(vertex_name, g, u.descriptor(), name);
pathIDs.push_back(name);
paths.push_back(mergePaths(paths, overlapMap, *it));
// Remove the merged paths.
for (ContigPath::const_iterator it2 = it->begin();
it2 != it->end(); ++it2) {
if (isPath(*it2))
paths[it2->id() - Vertex::s_offset].clear();
}
}
g_contigNames.lock();
}
/** Add the path overlap edges to the specified graph. */
static void addPathOverlapEdges(Graph& g,
const Paths& paths, const vector<string>& pathIDs,
const Overlaps& overlaps)
{
typedef graph_traits<Graph>::vertex_descriptor V;
const bool allowParallelEdge = opt::mode == opt::ASSEMBLE;
// Add the path vertices.
g_contigNames.unlock();
for (Paths::const_iterator it = paths.begin();
it != paths.end(); ++it) {
const ContigPath& path = *it;
const string& id = pathIDs[it - paths.begin()];
if (!path.empty()) {
V u = merge(g, path.begin(), path.end());
put(vertex_name, g, u, id);
}
}
g_contigNames.lock();
// Remove the single-end contigs that are in paths.
for (Paths::const_iterator it = paths.begin();
it != paths.end(); ++it)
remove_vertex_if(g, it->begin(), it->end(),
not1(std::mem_fun_ref(&ContigNode::ambiguous)));
// Add the path edges.
for (Overlaps::const_iterator it = overlaps.begin();
it != overlaps.end(); ++it) {
V u = it->source.descriptor();
V v = it->target.descriptor();
if (allowParallelEdge || !edge(u, v, g).second)
add_edge(u, v, it->distance, static_cast<DG&>(g));
else if (opt::verbose > 0)
cerr << "ambiguous overlap: " << get(vertex_name, g, u)
<< " -> " << get(vertex_name, g, v) << '\n';
}
}