/** Remove ambiguous contigs from the ends of the path. */
static void removeAmbiguousContigs(ContigPath& path)
{
if (!path.empty() && path.back().ambiguous())
path.erase(path.end() - 1);
if (!path.empty() && path.front().ambiguous())
path.erase(path.begin());
}
/** Merge the paths of the specified seed path.
* @return the merged contig path
*/
static ContigPath mergePath(const Lengths& lengths,
const ContigPathMap& paths, const ContigPath& seedPath)
{
assert(!seedPath.empty());
ContigNode seed1 = seedPath.front();
ContigPathMap::const_iterator path1It
= paths.find(seed1.contigIndex());
assert(path1It != paths.end());
ContigPath path(path1It->second);
if (seedPath.front().sense())
reverseComplement(path.begin(), path.end());
if (opt::verbose > 1)
#pragma omp critical(cout)
cout << "\n* " << seedPath << '\n'
<< get(g_contigNames, seedPath.front())
<< '\t' << path << '\n';
for (ContigPath::const_iterator it = seedPath.begin() + 1;
it != seedPath.end(); ++it) {
ContigNode seed2 = *it;
ContigPathMap::const_iterator path2It
= paths.find(seed2.contigIndex());
assert(path2It != paths.end());
ContigPath path2 = path2It->second;
if (seed2.sense())
reverseComplement(path2.begin(), path2.end());
ContigNode pivot
= find(path.begin(), path.end(), seed2) != path.end()
? seed2 : seed1;
ContigPath consensus = align(lengths, path, path2, pivot);
if (consensus.empty()) {
// This seed could be removed from the seed path.
if (opt::verbose > 1)
#pragma omp critical(cout)
cout << get(g_contigNames, seed2)
<< '\t' << path2 << '\n'
<< "\tinvalid\n";
} else {
path.swap(consensus);
if (opt::verbose > 1)
#pragma omp critical(cout)
cout << get(g_contigNames, seed2)
<< '\t' << path2 << '\n'
<< '\t' << path << '\n';
}
seed1 = seed2;
}
return path;
}
/** Read contig paths from the specified file.
* @param g the contig adjacency graph
* @param inPath the file of contig paths
* @param[out] pathIDs the path IDs
* @return the paths
*/
static Paths readPaths(Graph& g,
const string& inPath, vector<string>& pathIDs)
{
typedef graph_traits<Graph>::vertex_descriptor V;
assert(pathIDs.empty());
ifstream fin(inPath.c_str());
if (opt::verbose > 0)
cerr << "Reading `" << inPath << "'..." << endl;
if (inPath != "-")
assert_good(fin, inPath);
istream& in = inPath == "-" ? cin : fin;
assert_good(in, inPath);
Paths paths;
string id;
ContigPath path;
while (in >> id >> path) {
if (path.empty()) {
// Remove this contig from the graph.
V u = find_vertex(id, false, g);
clear_vertex(u, g);
remove_vertex(u, g);
} else {
pathIDs.push_back(id);
paths.push_back(path);
}
}
assert(in.eof());
return paths;
}
/** Attempt to merge the paths specified in mergeQ with path.
* @return the number of paths merged
*/
static unsigned mergePaths(const Lengths& lengths,
ContigPath& path,
deque<ContigNode>& mergeQ, set<ContigNode>& seen,
const ContigPathMap& paths)
{
unsigned merged = 0;
deque<ContigNode> invalid;
for (ContigNode pivot; !mergeQ.empty(); mergeQ.pop_front()) {
pivot = mergeQ.front();
ContigPathMap::const_iterator path2It
= paths.find(pivot.contigIndex());
if (path2It == paths.end())
continue;
ContigPath path2 = path2It->second;
if (pivot.sense())
reverseComplement(path2.begin(), path2.end());
ContigPath consensus = align(lengths, path, path2, pivot);
if (consensus.empty()) {
invalid.push_back(pivot);
continue;
}
appendToMergeQ(mergeQ, seen, path2);
path.swap(consensus);
if (gDebugPrint)
#pragma omp critical(cout)
cout << get(g_contigNames, pivot)
<< '\t' << path2 << '\n'
<< '\t' << path << '\n';
merged++;
}
mergeQ.swap(invalid);
return merged;
}
/** Add an edge if the two paths overlap.
* @param pivot the pivot at which to seed the alignment
* @return whether an overlap was found
*/
static bool addOverlapEdge(const Lengths& lengths,
PathGraph& gout, ContigNode pivot,
ContigNode seed1, const ContigPath& path1,
ContigNode seed2, const ContigPath& path2)
{
assert(seed1 != seed2);
// Determine the orientation of the overlap edge.
dir_type orientation = DIR_X;
ContigPath consensus = align(lengths,
path1, path2, pivot, orientation);
if (consensus.empty())
return false;
assert(orientation != DIR_X);
if (orientation == DIR_B) {
// One of the paths subsumes the other. Use the order of the
// seeds to determine the orientation of the edge.
orientation = find(consensus.begin(), consensus.end(), seed1)
< find(consensus.begin(), consensus.end(), seed2)
? DIR_F : DIR_R;
}
assert(orientation == DIR_F || orientation == DIR_R);
// Add the edge.
ContigNode u = orientation == DIR_F ? seed1 : seed2;
ContigNode v = orientation == DIR_F ? seed2 : seed1;
bool added = false;
#pragma omp critical(gout)
if (!edge(u, v, gout).second) {
add_edge(u, v, gout);
added = true;
}
return added;
}
/** Merge a sequence of overlapping paths. */
static ContigPath mergePaths(const Paths& paths,
const OverlapMap& overlaps, const ContigPath& merge)
{
assert(!merge.empty());
ContigNode u = merge.front();
ContigPath path(getPath(paths, u));
for (ContigPath::const_iterator it = merge.begin() + 1;
it != merge.end(); ++it) {
ContigNode v = *it;
ContigPath vpath(getPath(paths, v));
unsigned overlap = getOverlap(overlaps, u, v);
assert(path.size() > overlap);
assert(vpath.size() > overlap);
assert(equal(path.end() - overlap, path.end(),
vpath.begin()));
path.insert(path.end(), vpath.begin() + overlap, vpath.end());
u = v;
}
return path;
}
/** Find a path for the specified distance estimates.
* @param out [out] the solution path
*/
static void handleEstimate(const Graph& g,
const EstimateRecord& er, bool dirIdx,
ContigPath& out)
{
if (er.estimates[dirIdx].empty())
return;
ContigNode origin(er.refID, dirIdx);
ostringstream vout_ss;
ostream bitBucket(NULL);
ostream& vout = opt::verbose > 0 ? vout_ss : bitBucket;
vout << "\n* " << get(vertex_name, g, origin) << '\n';
unsigned minNumPairs = UINT_MAX;
// generate the reachable set
Constraints constraints;
for (Estimates::const_iterator iter
= er.estimates[dirIdx].begin();
iter != er.estimates[dirIdx].end(); ++iter) {
ContigNode v = iter->first;
const DistanceEst& ep = iter->second;
minNumPairs = min(minNumPairs, ep.numPairs);
constraints.push_back(Constraint(v,
ep.distance + allowedError(ep.stdDev)));
}
vout << "Constraints:";
printConstraints(vout, g, constraints) << '\n';
ContigPaths solutions;
unsigned numVisited = 0;
constrainedSearch(g, origin, constraints, solutions, numVisited);
bool tooComplex = numVisited >= opt::maxCost;
bool tooManySolutions = solutions.size() > opt::maxPaths;
set<ContigID> repeats = findRepeats(er.refID, solutions);
if (!repeats.empty()) {
vout << "Repeats:";
for (set<ContigID>::const_iterator it = repeats.begin();
it != repeats.end(); ++it)
vout << ' ' << get(g_contigNames, *it);
vout << '\n';
}
unsigned numPossiblePaths = solutions.size();
if (numPossiblePaths > 0)
vout << "Paths: " << numPossiblePaths << '\n';
for (ContigPaths::iterator solIter = solutions.begin();
solIter != solutions.end();) {
vout << *solIter << '\n';
// Calculate the path distance to each node and see if
// it is within the estimated distance.
map<ContigNode, int> distanceMap
= makeDistanceMap(g, origin, *solIter);
// Remove solutions whose distance estimates are not correct.
unsigned validCount = 0, invalidCount = 0, ignoredCount = 0;
for (Estimates::const_iterator iter
= er.estimates[dirIdx].begin();
iter != er.estimates[dirIdx].end(); ++iter) {
ContigNode v = iter->first;
const DistanceEst& ep = iter->second;
vout << get(vertex_name, g, v) << ',' << ep << '\t';
map<ContigNode, int>::iterator dmIter
= distanceMap.find(v);
if (dmIter == distanceMap.end()) {
// This contig is a repeat.
ignoredCount++;
vout << "ignored\n";
continue;
}
// translate distance by -overlap to match
// coordinate space used by the estimate
int actualDistance = dmIter->second;
int diff = actualDistance - ep.distance;
unsigned buffer = allowedError(ep.stdDev);
bool invalid = (unsigned)abs(diff) > buffer;
bool repeat = repeats.count(v.contigIndex()) > 0;
bool ignored = invalid && repeat;
if (ignored)
ignoredCount++;
else if (invalid)
invalidCount++;
else
validCount++;
vout << "dist: " << actualDistance
<< " diff: " << diff
<< " buffer: " << buffer
<< " n: " << ep.numPairs
<< (ignored ? " ignored" : invalid ? " invalid" : "")
<< '\n';
}
if (invalidCount == 0 && validCount > 0)
++solIter;
else
solIter = solutions.erase(solIter);
}
vout << "Solutions: " << solutions.size();
if (tooComplex)
vout << " (too complex)";
if (tooManySolutions)
vout << " (too many solutions)";
vout << '\n';
ContigPaths::iterator bestSol = solutions.end();
int minDiff = 999999;
for (ContigPaths::iterator solIter = solutions.begin();
solIter != solutions.end(); ++solIter) {
map<ContigNode, int> distanceMap
= makeDistanceMap(g, origin, *solIter);
int sumDiff = 0;
for (Estimates::const_iterator iter
= er.estimates[dirIdx].begin();
iter != er.estimates[dirIdx].end(); ++iter) {
ContigNode v = iter->first;
const DistanceEst& ep = iter->second;
if (repeats.count(v.contigIndex()) > 0)
continue;
map<ContigNode, int>::iterator dmIter
= distanceMap.find(v);
assert(dmIter != distanceMap.end());
int actualDistance = dmIter->second;
int diff = actualDistance - ep.distance;
sumDiff += abs(diff);
}
if (sumDiff < minDiff) {
minDiff = sumDiff;
bestSol = solIter;
}
vout << *solIter
<< " length: " << calculatePathLength(g, origin, *solIter)
<< " sumdiff: " << sumDiff << '\n';
}
/** Lock the debugging stream. */
static pthread_mutex_t coutMutex = PTHREAD_MUTEX_INITIALIZER;
pthread_mutex_lock(&coutMutex);
stats.totalAttempted++;
g_minNumPairs = min(g_minNumPairs, minNumPairs);
if (tooComplex) {
stats.tooComplex++;
} else if (tooManySolutions) {
stats.tooManySolutions++;
} else if (numPossiblePaths == 0) {
stats.noPossiblePaths++;
} else if (solutions.empty()) {
stats.noValidPaths++;
} else if (repeats.count(er.refID) > 0) {
vout << "Repeat: " << get(vertex_name, g, origin) << '\n';
stats.repeat++;
} else if (solutions.size() > 1) {
ContigPath path
= constructAmbiguousPath(g, origin, solutions);
if (!path.empty()) {
if (opt::extend)
extend(g, path.back(), back_inserter(path));
vout << path << '\n';
if (opt::scaffold) {
out.insert(out.end(), path.begin(), path.end());
g_minNumPairsUsed
= min(g_minNumPairsUsed, minNumPairs);
}
}
stats.multiEnd++;
} else {
assert(solutions.size() == 1);
assert(bestSol != solutions.end());
ContigPath& path = *bestSol;
if (opt::verbose > 1)
printDistanceMap(vout, g, origin, path);
if (opt::extend)
extend(g, path.back(), back_inserter(path));
out.insert(out.end(), path.begin(), path.end());
stats.uniqueEnd++;
g_minNumPairsUsed = min(g_minNumPairsUsed, minNumPairs);
}
cout << vout_ss.str();
if (!out.empty())
assert(!out.back().ambiguous());
pthread_mutex_unlock(&coutMutex);
}
/** Identify paths subsumed by the specified path.
* @param overlaps [out] paths that are found to overlap
* @return the ID of the subsuming path
*/
static ContigID identifySubsumedPaths(const Lengths& lengths,
ContigPathMap::const_iterator path1It,
ContigPathMap& paths,
set<ContigID>& out,
set<ContigID>& overlaps)
{
ostringstream vout;
out.clear();
ContigID id(path1It->first);
const ContigPath& path = path1It->second;
if (gDebugPrint)
vout << get(g_contigNames, ContigNode(id, false))
<< '\t' << path << '\n';
for (ContigPath::const_iterator it = path.begin();
it != path.end(); ++it) {
ContigNode pivot = *it;
if (pivot.ambiguous() || pivot.id() == id)
continue;
ContigPathMap::iterator path2It
= paths.find(pivot.contigIndex());
if (path2It == paths.end())
continue;
ContigPath path2 = path2It->second;
if (pivot.sense())
reverseComplement(path2.begin(), path2.end());
ContigPath consensus = align(lengths, path, path2, pivot);
if (consensus.empty())
continue;
if (equalIgnoreAmbiguos(consensus, path)) {
if (gDebugPrint)
vout << get(g_contigNames, pivot)
<< '\t' << path2 << '\n';
out.insert(path2It->first);
} else if (equalIgnoreAmbiguos(consensus, path2)) {
// This path is larger. Use it as the seed.
return identifySubsumedPaths(lengths, path2It, paths, out,
overlaps);
} else if (isCycle(lengths, consensus)) {
// The consensus path is a cycle.
bool isCyclePath1 = isCycle(lengths, path);
bool isCyclePath2 = isCycle(lengths, path2);
if (!isCyclePath1 && !isCyclePath2) {
// Neither path is a cycle.
if (gDebugPrint)
vout << get(g_contigNames, pivot)
<< '\t' << path2 << '\n'
<< "ignored\t" << consensus << '\n';
overlaps.insert(id);
overlaps.insert(path2It->first);
} else {
// At least one path is a cycle.
if (gDebugPrint)
vout << get(g_contigNames, pivot)
<< '\t' << path2 << '\n'
<< "cycle\t" << consensus << '\n';
if (isCyclePath1 && isCyclePath2)
out.insert(path2It->first);
else if (!isCyclePath1)
overlaps.insert(id);
else if (!isCyclePath2)
overlaps.insert(path2It->first);
}
} else {
if (gDebugPrint)
vout << get(g_contigNames, pivot)
<< '\t' << path2 << '\n'
<< "ignored\t" << consensus << '\n';
overlaps.insert(id);
overlaps.insert(path2It->first);
}
}
cout << vout.str();
return id;
}
/** Find an equivalent region of the two specified paths.
* @param[out] orientation the orientation of the alignment
* @return the consensus sequence
*/
static ContigPath align(const Lengths& lengths,
const ContigPath& path1, const ContigPath& path2,
ContigNode pivot, dir_type& orientation)
{
if (&path1 == &path2) {
// Ignore the trivial alignment when aligning a path to
// itself.
} else if (path1 == path2) {
// These two paths are identical.
orientation = DIR_B;
return path1;
} else {
ContigPath::const_iterator it
= search(path1.begin(), path1.end(),
path2.begin(), path2.end());
if (it != path1.end()) {
// path2 is subsumed in path1.
// Determine the orientation of the edge.
orientation
= it == path1.begin() ? DIR_R
: it + path2.size() == path1.end() ? DIR_F
: DIR_B;
return path1;
}
}
// Find a suitable pivot.
if (find(path1.begin(), path1.end(), pivot) == path1.end()
|| find(path2.begin(), path2.end(), pivot)
== path2.end()) {
bool good;
tie(pivot, good) = findPivot(path1, path2);
if (!good)
return ContigPath();
}
assert(find(path1.begin(), path1.end(), pivot) != path1.end());
ContigPath::const_iterator it2 = find(path2.begin(), path2.end(),
pivot);
assert(it2 != path2.end());
if (&path1 != &path2) {
// The seed must be unique in path2, unless we're aligning a
// path to itself.
assert(count(it2+1, path2.end(), pivot) == 0);
}
ContigPath consensus;
for (ContigPath::const_iterator it1 = find_if(
path1.begin(), path1.end(),
bind2nd(equal_to<ContigNode>(), pivot));
it1 != path1.end();
it1 = find_if(it1+1, path1.end(),
bind2nd(equal_to<ContigNode>(), pivot))) {
if (&*it1 == &*it2) {
// We are aligning a path to itself, and this is the
// trivial alignment, which we'll ignore.
continue;
}
consensus = align(lengths,
path1, path2, it1, it2, orientation);
if (!consensus.empty())
return consensus;
}
return consensus;
}
/** Return the consensus sequence of the specified gap. */
static ContigPath fillGap(const Graph& g,
const AmbPathConstraint& apConstraint,
vector<bool>& seen,
ofstream& outFasta)
{
if (opt::verbose > 1)
cerr << "\n* "
<< get(vertex_name, g, apConstraint.source) << ' '
<< apConstraint.dist << "N "
<< get(vertex_name, g, apConstraint.dest) << '\n';
Constraints constraints;
constraints.push_back(Constraint(apConstraint.dest,
apConstraint.dist + opt::distanceError));
ContigPaths solutions;
unsigned numVisited = 0;
constrainedSearch(g, apConstraint.source,
constraints, solutions, numVisited);
bool tooComplex = numVisited >= opt::maxCost;
for (ContigPaths::iterator solIt = solutions.begin();
solIt != solutions.end(); solIt++)
solIt->insert(solIt->begin(), apConstraint.source);
ContigPath consensus;
bool tooManySolutions = solutions.size() > opt::numBranches;
if (tooComplex) {
stats.tooComplex++;
if (opt::verbose > 1)
cerr << solutions.size() << " paths (too complex)\n";
} else if (tooManySolutions) {
stats.numTooManySolutions++;
if (opt::verbose > 1)
cerr << solutions.size() << " paths (too many)\n";
} else if (solutions.empty()) {
stats.numNoSolutions++;
if (opt::verbose > 1)
cerr << "no paths\n";
} else if (solutions.size() == 1) {
if (opt::verbose > 1)
cerr << "1 path\n" << solutions.front() << '\n';
stats.numMerged++;
} else {
assert(solutions.size() > 1);
if (opt::verbose > 2)
copy(solutions.begin(), solutions.end(),
ostream_iterator<ContigPath>(cerr, "\n"));
else if (opt::verbose > 1)
cerr << solutions.size() << " paths\n";
consensus = align(g, solutions, outFasta);
if (!consensus.empty()) {
stats.numMerged++;
// Mark contigs that are used in a consensus.
markSeen(seen, solutions, true);
if (opt::verbose > 1)
cerr << consensus << '\n';
} else
stats.notMerged++;
}
return consensus;
}
