int main( int argc, char* argv[] ) {
using namespace GetOpt;
GetOpt_pp opts(argc, argv);
if(argc == 1 || opts >> OptionPresent('h',"help")){
printUsage();
}
opts >> OptionPresent('v', "verbose", options::verbose);
opts >> Option('i', "input-format", options::inputFormat, "");
opts >> Option('o', "output-format", options::outputFormat, "");
opts >> Option('a',"evolution-model", options::distMethod, "");
opts >> Option('m',"memory-size", options::memSize, -1);
opts >> OptionPresent('r',"rapidnj", options::rapidNJ);
opts >> Option('k',"rapidnj-mem", options::percentageMemoryUsage, "");
opts >> Option('d',"rapidnj-disk", options::cacheDir, "");
opts >> OptionPresent('s',"simplenj", options::simpleNJ);
opts >> OptionPresent('f', "no-rapiddist", options::fastdist);
opts >> Option('c',"cores", options::cores, -1);
opts >> Option('b',"bootstrap", options::replicates, -1);
opts >> Option('t',"alignment-type", options::inputtype, "");
opts >> OptionPresent('g', "gpu", options::gpu);
opts >> OptionPresent('n', "no-negative-length", options::negative_branches);
opts >> Option('x', "outfile", options::outputFile, "");
options::fastdist = !options::fastdist;
vector<string> fileNames;
opts >> GlobalOption(fileNames);
if(fileNames.size() < 1){
cerr << "ERROR: An input file must be specified!" << endl;
exit(1);
}
if(fileNames.size() > 1){
cerr << "ERROR: Only one input file can be specified!" << endl;
exit(1);
}
options::fileName = fileNames[0];
if(opts.options_remain()){
cerr << "ERROR: One or more options were not recognised!" << endl;
exit(0);
}
streambuf* sbuf;
ofstream fileOutStream;
if(options::outputFile != "") {
fileOutStream.open(options::outputFile.data(), fstream::out | fstream::in | fstream::binary | fstream::trunc);
if(!fileOutStream.is_open()){
cerr << "Could not open the output file \"" << options::outputFile << "\"\n";
exit(1);
}
sbuf = fileOutStream.rdbuf();
} else {
sbuf = cout.rdbuf();
}
ostream out(sbuf);
if(options::verbose){
cerr << "RapidNJ v. " << VERSION << endl;
if(sizeof(void*) == 4) {
cerr << "32 bit system detected." << endl;
} else {
cerr << "64 bit system detected." << endl;
}
}
configureNumberOfCores();
#ifdef __linux__
gettimeofday(&start, NULL);
#endif
if(options::inputFormat == ""){
// try to determine the input format
if (options::fileName.compare(options::fileName.length() - 4, 4, ".sth") == 0){
if(options::verbose){
cerr << "Input format determined as stockholm" << endl;
}
options::inputFormat="sth";
} else if (options::fileName.compare(options::fileName.length() - 3, 3, ".fa") == 0 ||
options::fileName.compare(options::fileName.length() - 6, 6, ".fasta") == 0) {
if(options::verbose) {
cerr << "Input format determined as FASTA" << endl;
}
options::inputFormat="fa";
} else {
options::inputFormat = guessPhylipType(options::fileName);
if(options::verbose){
cerr << "Input format determined as phylip ";
if(options::inputFormat == "pa"){
cerr << "alignment" << endl;
} else {
cerr << "distance matrix" << endl;
}
}
}
}
dataloader* dl = NULL;
ProgressBar* pb = new ProgressBar();
if(options::inputFormat == "pd"){
//input is a distance matrix.
if(options::replicates > -1) {
cerr << "ERROR: Cannot perform bootstrapping with a distance matrix input." << endl;
exit(1);
}
distanceMatrixInput = true;
matrixSize = getMatrixSize();
} else {
dl = loadAlignment();
matrixSize = dl->getSequenceCount();
distanceMatrixInput = false;
}
if(options::outputFormat == "m") {
double memSize = getMemSize();
double requiredMemory = 0;
if(dl == NULL) {
cerr << "ERROR: Both input and output format is a distance matrix." << endl;
exit(1);
}
if(dl->type == DNA) {
requiredMemory += matrixSize * dl->getSequenceLength() / 2.0;
} else {
requiredMemory += matrixSize * dl->getSequenceLength();
}
requiredMemory += matrixSize * matrixSize * (double)sizeof(distType);
if(memSize < requiredMemory || options::cacheDir != "") {
//use a disk matrix
if(options::verbose) {
cerr << "Using disk based matrix" << endl;
}
computeDistanceMatrix(true, out, true, dl);
} else {
computeDistanceMatrix(false, out, true, dl);
}
} else {
if(options::replicates > -1) {
pb->childProgress(1.0 / (options::replicates + 1.0));
}
polytree* tree = computeTree(out, dl, pb);
if(options::replicates > -1) {
bootstrapTree(out, tree, dl, pb);
tree->serialize_tree(out);
} else {
tree->serialize_tree(out);
}
delete tree;
}
if(!distanceMatrixInput) {
delete dl;
}
delete pb;
if(options::verbose){
cerr << endl;
//printTime("Total running time:");
}
out.flush();
if(fileOutStream.is_open()) {
fileOutStream.close();
}
return 0;
}
