int main (int argc, char ** argv)
{
//const clock_t begin_time = clock();
if (argc<3) {
print_usage ();
}
////////////////////////////////////////////////////////////
// Init parameters
//
std::string input_file_name;
std::string bv_file_name;
std::string output_file_name;
bool compress = false;
////////////////////////////////////////////////////////////
// Read command line arguments
//
int arg_pos = 1;
while (arg_pos < argc){
std::string flag = argv[arg_pos];
if (flag[0] != '-') {
if (input_file_name.empty()) {
input_file_name = flag;
} else if (bv_file_name.empty()){
bv_file_name = flag;
} else {
std::cerr << "The mandatory files are already set, unknown file " << flag << " -> ignore\n";
}
} else if (flag.compare("-o") == 0) {
arg_pos++;
output_file_name = argv[arg_pos];
} else if (flag.compare("-h") == 0) {
print_usage ();
return 0;
} else if (flag.compare("-v") == 0) {
std::cout << "\nextract_reads version " << version << "\n";
return 0;
} else {
std::cerr << "Unknown option " << flag << "\n";
print_usage ();
return (0);
}
arg_pos++;
}
if (input_file_name.empty()) {
std::cerr << "Error: An input file name is needed -> exit\n";
print_usage ();
return (0);
} else if (bv_file_name.empty()) {
std::cerr << "Error: A bv file name is needed -> exit\n";
print_usage ();
return (0);
}
////////////////////////////////////////////////////////////
// Open the given file to check its type (fasta, fastq, gzip ?)
//
ReadFile * read_file = NULL;
std::ifstream infile;
infile.open(input_file_name.c_str());
if (!infile.good()) {
std::cerr << "Cannot open file file " << input_file_name << " -> ignore\n";
}
// Check the first char
std::string basename = input_file_name.substr(input_file_name.rfind("/")+1);
char c = infile.get();
if (c == '>') {
infile.close();
read_file = new FastaFile(input_file_name, bv_file_name);
} else if (c == '@') {
infile.close();
read_file = new FastqFile(input_file_name, bv_file_name);
} else {
infile.close();
gzFile tmp_gz_file = (gzFile) gzopen(input_file_name.c_str(), "r");
if (!tmp_gz_file) {
std::cerr << "Cannot open file " << input_file_name << " -> ignore\n";
exit(1);
}
c = gzgetc(tmp_gz_file);
if (c == '>') {
gzclose(tmp_gz_file);
compress = true;
read_file = new GzFastaFile(input_file_name, bv_file_name);
} else if (c == '@') {
gzclose(tmp_gz_file);
compress = true;
read_file = new GzFastqFile(input_file_name, bv_file_name);
} else {
std::cerr << "Unknown format: " << input_file_name << " -> ignore\n";
}
}
////////////////////////////////////////////////////////////
// Open the output file and write selected reads in it
// Different behaviors if : - output file name is given
// - compress is true or not
//
if (compress) {
if (output_file_name.empty()) {
std::cerr << "Error, try to compress results but no output file name is given\n";
exit(1);
}
gzFile filetmp = (gzFile) gzopen(output_file_name.c_str(), "w6");
if (filetmp == NULL) {
std::cerr << "Error, cannot open file " << output_file_name << "\n";
}
std::string & current_read = read_file->get_next_read();
while (!current_read.empty()) {
gzprintf(filetmp, "%s", read_file->get_data().c_str());
current_read = read_file->get_next_read();
}
gzclose(filetmp);
} else {
if (!output_file_name.empty()) {
std::ofstream outfile;
outfile.open (output_file_name.c_str());
if (!outfile.good()) {
std::cerr << "Cannot write on file " << output_file_name << "\n";
return 1;
}
std::string & current_read = read_file->get_next_read();
while (!current_read.empty()) {
outfile << read_file->get_data();
current_read = read_file->get_next_read();
}
outfile.close();
} else {
std::string & current_read = read_file->get_next_read();
while (!current_read.empty()) {
std::cout << read_file->get_data();
current_read = read_file->get_next_read();
}
}
}
if (read_file != NULL) {
delete read_file;
}
return 0;
}