/** Align the specified pair of sequences.
* @return the number of matches and size of the consensus
*/
static pair<unsigned, unsigned> alignPair(
const string& seqa, const string& seqb)
{
NWAlignment alignment;
unsigned matches = alignGlobal(seqa, seqb, alignment);
if (opt::verbose > 2)
#pragma omp critical(cerr)
cerr << alignment;
return make_pair(matches, alignment.size());
}
/* 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;
}