int main(int argc, char* const* argv)
{
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 'l':
arg >> opt::k;
break;
case 'c':
arg >> opt::c;
break;
case 'd':
arg >> opt::distPath;
break;
case 'f':
arg >> opt::fragPath;
break;
case 'h':
arg >> opt::histPath;
break;
case 'v':
opt::verbose++;
break;
case OPT_HELP:
cout << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
cout << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
if (optarg != NULL && !arg.eof()) {
cerr << PROGRAM ": invalid option: `-"
<< (char)c << optarg << "'\n";
exit(EXIT_FAILURE);
}
}
if (opt::k <= 0 && opt::inputFormat == opt::KALIGNER) {
cerr << PROGRAM ": " << "missing -k,--kmer option\n";
die = true;
}
if (die) {
cerr << "Try `" << PROGRAM
<< " --help' for more information.\n";
exit(EXIT_FAILURE);
}
if (!opt::fragPath.empty()) {
fragFile.open(opt::fragPath.c_str());
assert(fragFile.is_open());
}
ReadAlignMap alignTable(1);
if (optind < argc) {
for_each(argv + optind, argv + argc,
bind2nd(ptr_fun(readAlignmentsFile), &alignTable));
} else {
if (opt::verbose > 0)
cerr << "Reading from standard input..." << endl;
readAlignments(cin, &alignTable);
}
if (opt::verbose > 0)
cerr << "Read " << stats.alignments << " alignments" << endl;
unsigned numRF = histogram.count(INT_MIN, 0);
unsigned numFR = histogram.count(1, INT_MAX);
size_t sum = alignTable.size()
+ stats.bothUnaligned + stats.oneUnaligned
+ numFR + numRF + stats.numFF
+ stats.numDifferent + stats.numMulti + stats.numSplit;
cerr <<
"Mateless " << percent(alignTable.size(), sum) << "\n"
"Unaligned " << percent(stats.bothUnaligned, sum) << "\n"
"Singleton " << percent(stats.oneUnaligned, sum) << "\n"
"FR " << percent(numFR, sum) << "\n"
"RF " << percent(numRF, sum) << "\n"
"FF " << percent(stats.numFF, sum) << "\n"
"Different " << percent(stats.numDifferent, sum) << "\n"
"Multimap " << percent(stats.numMulti, sum) << "\n"
"Split " << percent(stats.numSplit, sum) << "\n"
"Total " << sum << endl;
if (!opt::distPath.empty())
generateDistFile();
if (!opt::fragPath.empty())
fragFile.close();
if (!opt::histPath.empty()) {
ofstream histFile(opt::histPath.c_str());
assert(histFile.is_open());
histFile << histogram;
assert(histFile.good());
histFile.close();
}
if (numFR < numRF)
histogram = histogram.negate();
histogram.eraseNegative();
histogram.removeNoise();
histogram.removeOutliers();
Histogram h = histogram.trimFraction(0.0001);
if (opt::verbose > 0)
cerr << "Stats mean: " << setprecision(4) << h.mean() << " "
"median: " << setprecision(4) << h.median() << " "
"sd: " << setprecision(4) << h.sd() << " "
"n: " << h.size() << " "
"min: " << h.minimum() << " max: " << h.maximum() << '\n'
<< h.barplot() << endl;
if (stats.numFF > numFR && stats.numFF > numRF) {
cerr << "error: The mate pairs of this library are oriented "
"forward-forward (FF), which is not supported by ABySS."
<< endl;
exit(EXIT_FAILURE);
}
return 0;
}
int main(int argc, char** argv)
{
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 OPT_MIND:
arg >> opt::minDist;
break;
case OPT_MAXD:
arg >> opt::maxDist;
break;
case 'l':
arg >> opt::minAlign;
break;
case 'j': arg >> opt::threads; break;
case 'k': arg >> opt::k; break;
case 'n': arg >> opt::npairs; break;
case 'o': arg >> opt::out; break;
case 'q': arg >> opt::minMapQ; break;
case 's': arg >> opt::seedLen; break;
case 'v': opt::verbose++; break;
case OPT_HELP:
cout << USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
cout << VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
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 (opt::seedLen <= 0) {
cerr << PROGRAM ": missing -s,--seed-length option\n";
die = true;
}
if (opt::npairs <= 0) {
cerr << PROGRAM ": missing -n,--npairs option\n";
die = true;
}
if (argc - optind < 1) {
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);
}
if (opt::seedLen < 2*opt::k)
cerr << "warning: the seed-length should be at least twice k:"
" k=" << opt::k << ", s=" << opt::seedLen << '\n';
assert(opt::minAlign > 0);
#if _OPENMP
if (opt::threads > 0)
omp_set_num_threads(opt::threads);
#endif
string distanceCountFile(argv[optind++]);
string alignFile(argv[optind] == NULL ? "-" : argv[optind++]);
ifstream inFile(alignFile.c_str());
istream& in(strcmp(alignFile.c_str(), "-") == 0 ? cin : inFile);
if (strcmp(alignFile.c_str(), "-") != 0)
assert_good(inFile, alignFile);
ofstream outFile;
if (!opt::out.empty()) {
outFile.open(opt::out.c_str());
assert(outFile.is_open());
}
ostream& out = opt::out.empty() ? cout : outFile;
if (opt::format == DOT)
out << "digraph dist {\ngraph ["
"k=" << opt::k << " "
"s=" << opt::seedLen << " "
"n=" << opt::npairs << "]\n";
// The fragment size histogram may not be written out until after
// the alignments complete. Wait for the alignments to complete.
in.peek();
// Read the fragment size distribution.
Histogram distanceHist = loadHist(distanceCountFile);
unsigned numRF = distanceHist.count(INT_MIN, 0);
unsigned numFR = distanceHist.count(1, INT_MAX);
unsigned numTotal = distanceHist.size();
bool libRF = numFR < numRF;
if (opt::verbose > 0) {
cerr << "Mate orientation FR: " << numFR << setprecision(3)
<< " (" << (float)100*numFR/numTotal << "%)"
<< " RF: " << numRF << setprecision(3)
<< " (" << (float)100*numRF/numTotal << "%)\n"
<< "The library " << distanceCountFile << " is oriented "
<< (libRF
? "reverse-forward (RF)" : "forward-reverse (FR)")
<< ".\n";
}
// Determine the orientation of the library.
if (opt::rf == -1)
opt::rf = libRF;
if (opt::rf)
distanceHist = distanceHist.negate();
if (opt::rf != libRF)
cerr << "warning: The orientation is forced to "
<< (opt::rf
? "reverse-forward (RF)" : "forward-reverse (FR)")
<< " which differs from the detected orientation.\n";
distanceHist.eraseNegative();
distanceHist.removeNoise();
distanceHist.removeOutliers();
Histogram h = distanceHist.trimFraction(0.0001);
if (opt::verbose > 0)
cerr << "Stats mean: " << setprecision(4) << h.mean() << " "
"median: " << setprecision(4) << h.median() << " "
"sd: " << setprecision(4) << h.sd() << " "
"n: " << h.size() << " "
"min: " << h.minimum() << " max: " << h.maximum() << '\n'
<< h.barplot() << endl;
PMF pmf(h);
if (opt::minDist == numeric_limits<int>::min())
opt::minDist = -opt::k + 1;
if (opt::maxDist == numeric_limits<int>::max())
opt::maxDist = pmf.maxValue();
if (opt::verbose > 0)
cerr << "Minimum and maximum distance are set to "
<< opt::minDist << " and " << opt::maxDist << " bp.\n";
assert(opt::minDist < opt::maxDist);
// Read the contig lengths.
vector<unsigned> contigLens;
readContigLengths(in, contigLens);
g_contigNames.lock();
// Estimate the distances between contigs.
istream_iterator<SAMRecord> it(in), last;
if (contigLens.size() == 1) {
// When mapping to a single contig, no alignments spanning
// contigs are expected.
assert(in.eof());
exit(EXIT_SUCCESS);
}
assert(in);
g_recMA = opt::minAlign;
#pragma omp parallel
for (vector<SAMRecord> records;;) {
records.clear();
#pragma omp critical(in)
readPairs(it, last, records);
if (records.empty())
break;
writeEstimates(out, records, contigLens, pmf);
}
if (opt::verbose > 0) {
float prop_dups = (float)100 * stats.dup_frags / stats.total_frags;
cerr << "Duplicate rate of spanning fragments: "
<< stats.dup_frags << "/"
<< stats.total_frags << " ("
<< setprecision(3) << prop_dups << "%)\n";
if (prop_dups > 0.5)
cerr << PROGRAM << ": warning: duplicate rate of fragments "
"spanning more than one contig is high.\n";
}
if (opt::verbose > 0 && g_recMA != opt::minAlign)
cerr << PROGRAM << ": warning: MLE will be more accurate if "
"l is decreased to " << g_recMA << ".\n";
assert(in.eof());
if (opt::format == DOT)
out << "}\n";
return 0;
}
