int runMe(int argc, char* argv[]) {
ArgProcessor args(argc, argv);
if(args.isArgSet("--help") ||
(!(args.isArgSet("--reads")
&&
( args.isArgSet("--kmers") || args.isArgSet("--kmers_from_reads") )
)) ) {
cerr << usage(args) << endl << endl;
exit(1);
}
string reads_fasta_file = args.getStringVal("--reads");
bool is_DS = (! args.isArgSet("--SS"));
if(args.isArgSet("--kmer_size")) {
KMER_SIZE = args.getIntVal("--kmer_size");
if(KMER_SIZE < 20) {
cerr << "Error, min kmer size is 20";
exit(2);
}
}
if(args.isArgSet("--monitor")) {
IRKE_COMMON::MONITOR = args.getIntVal("--monitor");
}
if (args.isArgSet("--num_threads")) {
int num_threads = args.getIntVal("--num_threads");
if (num_threads < MAX_THREADS) {
omp_set_num_threads(num_threads);
}
else {
// set to max
omp_set_num_threads(MAX_THREADS);
}
}
if(omp_get_max_threads() > MAX_THREADS) {
omp_set_num_threads(MAX_THREADS);
}
KmerCounter kcounter (KMER_SIZE, is_DS);
if (args.isArgSet("--kmers")) {
string kmers_fasta_file = args.getStringVal("--kmers");
populate_kmer_counter_from_kmers(kcounter, kmers_fasta_file);
}
else {
string kmer_read_source_fasta_file = args.getStringVal("--kmers_from_reads");
populate_kmer_counter_from_reads(kcounter, kmer_read_source_fasta_file);
}
Fasta_reader fasta_reader(reads_fasta_file);
bool write_coverage_info = args.isArgSet("--capture_coverage_info");
int start_time = time(NULL);
#pragma omp parallel
while (true) {
if (! fasta_reader.hasNext())
break;
int myTid = omp_get_thread_num();
Fasta_entry fe = fasta_reader.getNext();
string sequence = fe.get_sequence();
if(sequence == "")
continue;
string header = fe.get_header();
vector<unsigned int> kmer_coverage = compute_kmer_coverage(sequence, kcounter);
unsigned int median_cov = median_coverage(kmer_coverage);
float mean_cov = mean(kmer_coverage);
float stdev = stDev(kmer_coverage);
float pct_stdev_of_avg = stdev/mean_cov*100;
stringstream stats_text;
stats_text << median_cov << "\t"
<< mean_cov << "\t"
<< stdev << "\t"
<< pct_stdev_of_avg << "\t"
<< fe.get_accession();
stats_text << "\tthread:" << myTid;
if(write_coverage_info) {
// add the coverage info
stats_text << "\t";
for (size_t i = 0; i < kmer_coverage.size(); i++) {
stats_text<< kmer_coverage[i];
if(i != kmer_coverage.size() - 1) {
stats_text<< ",";
}
}
}
stats_text << endl;
#pragma omp critical
{
cout << stats_text.str();
}
if (mean_cov < 0) {
cerr << "ERROR, cannot have negative coverage!!" << endl;
exit(1);
}
}
int end_time = time(NULL);
cerr << "STATS_GENERATION_TIME: " << (end_time - start_time) << " seconds." << endl;
return(0);
}
int main(int argc, char* argv[]) {
ArgProcessor args(argc, argv);
if(args.isArgSet("--help") ||
(!(args.isArgSet("--reads") && args.isArgSet("--kmers")))) {
cerr << usage(args) << endl << endl;
exit(1);
}
string reads_fasta_file = args.getStringVal("--reads");
string kmers_fasta_file = args.getStringVal("--kmers");
bool is_DS = (! args.isArgSet("--SS"));
if(args.isArgSet("--kmer_size")) {
KMER_SIZE = args.getIntVal("--kmer_size");
if(KMER_SIZE < 20) {
cerr << "Error, min kmer size is 20";
exit(2);
}
}
if(args.isArgSet("--monitor")) {
IRKE_COMMON::MONITOR = args.getIntVal("--monitor");
}
if(omp_get_max_threads() > MAX_THREADS) {
omp_set_num_threads(MAX_THREADS);
}
KmerCounter kcounter (KMER_SIZE, is_DS);
populate_kmer_counter(kcounter, kmers_fasta_file);
Fasta_reader fasta_reader(reads_fasta_file);
ofstream* filewriter = NULL;
ofstream* covwriter = NULL;
bool write_coverage_info = args.isArgSet("--capture_coverage_info");
while (true) {
Fasta_entry fe = fasta_reader.getNext();
string sequence = fe.get_sequence();
if(sequence == "") break;
string header = fe.get_header();
vector<unsigned int> kmer_coverage = compute_kmer_coverage(sequence, kcounter);
unsigned int median_cov = median_coverage(kmer_coverage);
float mean_cov = mean(kmer_coverage);
float stdev = stDev(kmer_coverage);
float pct_stdev_of_avg = stdev/mean_cov*100;
stringstream stats_text;
stats_text << median_cov << "\t"
<< mean_cov << "\t"
<< stdev << "\t"
<< pct_stdev_of_avg << "\t"
<< fe.get_accession();
if(write_coverage_info) {
// add the coverage info
stats_text << "\t";
for (int i = 0; i < kmer_coverage.size(); i++) {
stats_text<< kmer_coverage[i];
if(i != kmer_coverage.size() - 1) {
stats_text<< ",";
}
}
}
stats_text << endl;
cout << stats_text.str();
if (mean_cov < 0) {
cerr << "ERROR, cannot have negative coverage!!" << endl;
exit(1);
}
}
return(0);
}
