/** 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;
}
/** Return an ambiguous path that agrees with all the given paths. */
static ContigPath constructAmbiguousPath(const Graph &g,
const ContigNode& origin, const ContigPaths& paths)
{
assert(!paths.empty());
// Find the size of the smallest path.
const ContigPath& firstSol = paths.front();
size_t min_len = firstSol.size();
for (ContigPaths::const_iterator it = paths.begin() + 1;
it != paths.end(); ++it)
min_len = min(min_len, it->size());
// Find the longest prefix.
ContigPath vppath;
size_t longestPrefix;
bool commonPrefix = true;
for (longestPrefix = 0;
longestPrefix < min_len; longestPrefix++) {
const ContigNode& common_path_node = firstSol[longestPrefix];
for (ContigPaths::const_iterator solIter = paths.begin();
solIter != paths.end(); ++solIter) {
const ContigNode& pathnode = (*solIter)[longestPrefix];
if (pathnode != common_path_node) {
// Found the longest prefix.
commonPrefix = false;
break;
}
}
if (!commonPrefix)
break;
vppath.push_back(common_path_node);
}
// Find the longest suffix.
ContigPath vspath;
size_t longestSuffix;
bool commonSuffix = true;
for (longestSuffix = 0;
longestSuffix < min_len-longestPrefix; longestSuffix++) {
const ContigNode& common_path_node
= firstSol[firstSol.size()-longestSuffix-1];
for (ContigPaths::const_iterator solIter = paths.begin();
solIter != paths.end(); ++solIter) {
const ContigNode& pathnode
= (*solIter)[solIter->size()-longestSuffix-1];
if (pathnode != common_path_node) {
// Found the longest suffix.
commonSuffix = false;
break;
}
}
if (!commonSuffix)
break;
vspath.push_back(common_path_node);
}
ContigPath out;
out.reserve(vppath.size() + 1 + vspath.size());
out.insert(out.end(), vppath.begin(), vppath.end());
if (longestSuffix > 0) {
const ContigPath& longestPath(
*max_element(paths.begin(), paths.end(),
ComparePathLength(g, origin)));
unsigned length = calculatePathLength(g, origin, longestPath,
longestPrefix, longestSuffix);
// Account for the overlap on the right.
int dist = length + getDistance(g,
longestSuffix == longestPath.size() ? origin
: *(longestPath.rbegin() + longestSuffix),
*(longestPath.rbegin() + longestSuffix - 1));
// Add k-1 because it is the convention.
int numN = dist + opt::k - 1;
assert(numN > 0);
out.push_back(ContigNode(numN, 'N'));
out.insert(out.end(), vspath.rbegin(), vspath.rend());
}
return out;
}
/* 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;
}
