/** Merge the specified seed paths. * @return the merged contig paths */ static ContigPaths mergeSeedPaths(const Lengths& lengths, const ContigPathMap& paths, const ContigPaths& seedPaths) { if (opt::verbose > 0) cout << "\nMerging paths\n"; ContigPaths out; out.reserve(seedPaths.size()); for (ContigPaths::const_iterator it = seedPaths.begin(); it != seedPaths.end(); ++it) out.push_back(mergePath(lengths, paths, *it)); return out; }
/** 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); }
/** 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; }
/* Resolve ambiguous region using pairwise alignment * (Needleman-Wunsch) ('solutions' contain exactly two paths, from a * source contig to a dest contig) */ static ContigPath alignPair(const Graph& g, const ContigPaths& solutions, ofstream& out) { assert(solutions.size() == 2); assert(solutions[0].size() > 1); assert(solutions[1].size() > 1); assert(solutions[0].front() == solutions[1].front()); assert(solutions[0].back() == solutions[1].back()); ContigPath fstSol(solutions[0].begin()+1, solutions[0].end()-1); ContigPath sndSol(solutions[1].begin()+1, solutions[1].end()-1); if (fstSol.empty() || sndSol.empty()) { // This entire sequence may be deleted. const ContigPath& sol(fstSol.empty() ? sndSol : fstSol); assert(!sol.empty()); Sequence consensus(mergePath(g, sol)); assert(consensus.size() > opt::k - 1); string::iterator first = consensus.begin() + opt::k - 1; transform(first, consensus.end(), first, ::tolower); unsigned match = opt::k - 1; float identity = (float)match / consensus.size(); if (opt::verbose > 2) cerr << consensus << '\n'; if (opt::verbose > 1) cerr << identity << (identity < opt::identity ? " (too low)\n" : "\n"); if (identity < opt::identity) return ContigPath(); unsigned coverage = calculatePathProperties(g, sol).coverage; ContigNode u = outputNewContig(g, solutions, 1, 1, consensus, coverage, out); ContigPath path; path.push_back(solutions.front().front()); path.push_back(u); path.push_back(solutions.front().back()); return path; } Sequence fstPathContig(mergePath(g, fstSol)); Sequence sndPathContig(mergePath(g, sndSol)); if (fstPathContig == sndPathContig) { // These two paths have identical sequence. if (fstSol.size() == sndSol.size()) { // A perfect match must be caused by palindrome. typedef ContigPath::const_iterator It; pair<It, It> it = mismatch( fstSol.begin(), fstSol.end(), sndSol.begin()); assert(it.first != fstSol.end()); assert(it.second != sndSol.end()); assert(*it.first == get(vertex_complement, g, *it.second)); assert(equal(it.first+1, It(fstSol.end()), it.second+1)); if (opt::verbose > 1) cerr << "Palindrome: " << get(vertex_contig_name, g, *it.first) << '\n'; return solutions[0]; } else { // The paths are different lengths. cerr << PROGRAM ": warning: " "Two paths have identical sequence, which may be " "caused by a transitive edge in the overlap graph.\n" << '\t' << fstSol << '\n' << '\t' << sndSol << '\n'; return solutions[fstSol.size() > sndSol.size() ? 0 : 1]; } } unsigned minLength = min( fstPathContig.length(), sndPathContig.length()); unsigned maxLength = max( fstPathContig.length(), sndPathContig.length()); float lengthRatio = (float)minLength / maxLength; if (lengthRatio < opt::identity) { if (opt::verbose > 1) cerr << minLength << '\t' << maxLength << '\t' << lengthRatio << "\t(different length)\n"; return ContigPath(); } NWAlignment align; unsigned match = alignGlobal(fstPathContig, sndPathContig, align); float identity = (float)match / align.size(); if (opt::verbose > 2) cerr << align; if (opt::verbose > 1) cerr << identity << (identity < opt::identity ? " (too low)\n" : "\n"); if (identity < opt::identity) return ContigPath(); unsigned coverage = calculatePathProperties(g, fstSol).coverage + calculatePathProperties(g, sndSol).coverage; ContigNode u = outputNewContig(g, solutions, 1, 1, align.consensus(), coverage, out); ContigPath path; path.push_back(solutions.front().front()); path.push_back(u); path.push_back(solutions.front().back()); return path; }