/** Index the first and last contig of each path to facilitate finding
* overlaps between paths. */
static SeedMap makeSeedMap(const Paths& paths)
{
SeedMap seedMap;
for (Paths::const_iterator it = paths.begin();
it != paths.end(); ++it) {
if (it->empty())
continue;
assert(!it->front().ambiguous());
seedMap.insert(make_pair(it->front(),
Vertex(it - paths.begin(), false)));
assert(!it->back().ambiguous());
seedMap.insert(make_pair(it->back() ^ 1,
Vertex(it - paths.begin(), true)));
}
return seedMap;
}
int main(int argc, char** argv)
{
string commandLine;
{
ostringstream ss;
char** last = argv + argc - 1;
copy(argv, last, ostream_iterator<const char *>(ss, " "));
ss << *last;
commandLine = ss.str();
}
if (!opt::db.empty())
opt::metaVars.resize(3);
bool die = false;
for (int c; (c = getopt_long(argc, argv,
shortopts, longopts, NULL)) != -1;) {
istringstream arg(optarg != NULL ? optarg : "");
switch (c) {
case '?': die = true; break;
case 'g': arg >> opt::graphPath; break;
case 'k': arg >> opt::k; break;
case 'r': arg >> opt::repeatContigs; break;
case 'v': opt::verbose++; break;
case OPT_HELP:
cout << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
cout << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_DB:
arg >> opt::db; break;
case OPT_LIBRARY:
arg >> opt::metaVars[0]; break;
case OPT_STRAIN:
arg >> opt::metaVars[1]; break;
case OPT_SPECIES:
arg >> opt::metaVars[2]; break;
}
if (optarg != NULL && !arg.eof()) {
cerr << PROGRAM ": invalid option: `-"
<< (char)c << optarg << "'\n";
exit(EXIT_FAILURE);
}
}
if (opt::k <= 0) {
cerr << PROGRAM ": missing -k,--kmer option\n";
die = true;
}
if (argc - optind < 2) {
cerr << PROGRAM ": missing arguments\n";
die = true;
} else if (argc - optind > 2) {
cerr << PROGRAM ": too many arguments\n";
die = true;
}
if (die) {
cerr << "Try `" << PROGRAM
<< " --help' for more information.\n";
exit(EXIT_FAILURE);
}
const char *adjPath = argv[optind++];
if (opt::verbose > 0)
cerr << "Reading `" << adjPath << "'..." << endl;
ifstream fin(adjPath);
assert_good(fin, adjPath);
Graph g;
fin >> g;
Vertex::s_offset = g.num_vertices() / 2;
string pathsFile(argv[optind++]);
vector<string> pathIDs;
Paths paths = readPaths(g, pathsFile, pathIDs);
switch (opt::mode) {
case opt::OVERLAP:
// Find overlapping paths, do not assemble.
addPathOverlapEdges(g, paths, pathIDs,
findOverlaps(g, paths));
paths.clear();
if (opt::graphPath.empty())
opt::graphPath = "-";
break;
case opt::ASSEMBLE:
// Assemble overlapping paths.
assembleOverlappingPaths(g, paths, pathIDs);
break;
case opt::TRIM:
// Trim overlapping paths.
trimOverlaps(g, paths);
// Remove paths consisting of a single contig.
for_each_if(paths.begin(), paths.end(),
mem_fun_ref(&ContigPath::clear),
compose1(
bind2nd(equal_to<ContigPath::size_type>(), 1),
mem_fun_ref(&ContigPath::size)));
// Add the paths to the graph.
addPathOverlapEdges(g, paths, pathIDs, Overlaps());
break;
}
// Output the paths.
for (Paths::const_iterator it = paths.begin();
it != paths.end(); ++it) {
if (it->empty())
continue;
assert(it->size() != 1);
cout << pathIDs[it - paths.begin()] << '\t' << *it << '\n';
}
assert(cout.good());
// Output the graph.
if (!opt::graphPath.empty()) {
ofstream fout;
ostream& out = opt::graphPath == "-" ? cout
: (fout.open(opt::graphPath.c_str()), fout);
assert_good(out, opt::graphPath);
write_graph(out, g, PROGRAM, commandLine);
assert_good(out, opt::graphPath);
}
// Output the repeat contigs.
if (!opt::repeatContigs.empty()) {
sort(s_trimmedContigs.begin(), s_trimmedContigs.end());
s_trimmedContigs.erase(
unique(s_trimmedContigs.begin(),
s_trimmedContigs.end()), s_trimmedContigs.end());
ofstream out(opt::repeatContigs.c_str());
assert_good(out, opt::repeatContigs);
for (vector<ContigID>::const_iterator it
= s_trimmedContigs.begin();
it != s_trimmedContigs.end(); ++it)
out << get(g_contigNames, *it) << '\n';
assert_good(out, opt::repeatContigs);
}
if (!opt::db.empty()) {
init(db,
opt::db,
opt::verbose,
PROGRAM,
opt::getCommand(argc, argv),
opt::metaVars);
addToDb(db, "SS", opt::ss);
addToDb(db, "K", opt::k);
}
return 0;
}