int main(int argc, char *argv[]) {
try {
if (argc == 1) usage();
Initial_Time();
std::cerr << "Start at: " << Curr_Time() << std::endl;
int noptions = mGetOptions(argc, argv);
#if defined (_OPENMP)
if (param.ncpu) omp_set_num_threads(param.ncpu);
#endif
finDB.open(refseqFile.c_str());
if (!finDB) {
std::cerr << "fatal error: failed to open ref file\n";
exit(1);
}
ref.Run_ConvertBinseq(finDB);
std::cerr << "Load in "
<< ref.total_num
<< " reference seqs, total size "
<< ref.sum_length
<< " bp. "
<< Cal_AllTime()
<< " secs passed"
<< std::endl;
ref.CreateIndex();
std::cerr << "Create refseq k-mer index table. "
<< Cal_AllTime()
<< " secs passed"
<< std::endl;
RunProcess();
} catch (const std::exception & e) {
std::cerr << e.what() << std::endl;
return 1;
}
return 0;
}
int HomoAndMicrosateDis(int argc, char *argv[]) {
if (argc == 1) DisUsage();
for (int i=0; i<argc; i++) {
std::cout <<argv[i]<<' ';
}
Initial_Time();
std::cout <<"Start at: "<<Curr_Time()<< std::endl;
int noptions = dGetOptions(argc, argv);
// process user defined region
if (!one_region.empty()) {
if (!polyscan.ParseOneRegion(one_region)) {
std::cerr<<"fatal error: Please give correct defined region format (-r) \n";
exit(1);
}
polyscan.ifUserDefinedRegion = true;
} else {
polyscan.ifUserDefinedRegion = false;
}
// reading bed file if is exist
finB.open(bedFile.c_str());
if (finB) {
std::cout << "loading bed regions ..." << std::endl;
polyscan.LoadBeds(finB);
polyscan.BedFilterorNot();
}
// check bam list file
finM.open(bamListFile.c_str());
if (!finM) {
std::cerr<<"fatal error: failed to open bam list file\n";
exit(1);
}
std::cout << "loading bam list ..." << std::endl;
polyscan.LoadBams(finM);
// check h**o/microsate file
finH.open(homoFile.c_str());
if (!finH) {
std::cerr<<"fatal error: failed to open homopolymer and microsatellites file\n";
exit(1);
}
std::cout << "loading homopolymer and microsatellite sites ..." << std::endl;
polyscan.LoadHomosAndMicrosates(finH);
finH.close();
//polyscan.TestHomos();
polyscan.SplitWindows();
//polyscan.TestWindows();
std::cout << "\nTotal loading windows: " << polyscan.totalWindowsNum << " \n\n";
std::cout << "\nTotal loading homopolymer and microsatellites: " << polyscan.totalHomosites << " \n\n";
// pour out distribution
foutD.open( disFile.c_str() );
if (!foutD) {
std::cerr <<"failed to open file: "<<disFile<< std::endl;
exit(1);
}
polyscan.GetHomoDistribution(foutD);
foutD.close();
std::cout << "\nTotal time consumed: " << Cal_AllTime() << " secs\n\n";
return 0;
}
// Scan homosites and windows
void RefSeq::ScanHomoAndMicrosate(std::ifstream &fin) {
_seq.resize(param.max_dbseq_size);
total_num = sum_length = 0;
unsigned int index = 0;
_count = 0;
while (LoadNextSeq(fin)) {
// filtering little reference sequences
if (_length < 20 ) continue;
RefTitle r;
r._name =_name;
r._size = _length;
title.push_back(r);
// scan window and homopolymer site
DoScan(_length, _name, index);
std::cout << "scanning chomosome "
<< _name << " done. "
<< Cal_AllTime() << " secs passed" << std::endl;
index++;
total_num++;
sum_length += _length;
}
_seq.clear();
}
int HomoAndMicrosateDisMsi(int argc, char *argv[]) {
if (argc == 1) DisUsage();
for (int i=0; i<argc; i++) {
std::cout <<argv[i]<<' ';
}
Initial_Time();
std::cout <<"Start at: "<<Curr_Time() << std::endl;
int noptions = dGetOptions(argc, argv);
// process user defined region
if (!one_region.empty()) {
if (!polyscan.ParseOneRegion(one_region)) {
std::cerr<<"fatal error: Please give correct defined region format (-r) \n";
exit(1);
}
polyscan.ifUserDefinedRegion = true;
} else {
polyscan.ifUserDefinedRegion = false;
}
// reading bed file if is exist
finB.open(bedFile.c_str());
if (finB) {
std::cout << "loading bed regions ..." << std::endl;
polyscan.LoadBeds(finB);
polyscan.BedFilterorNot();
}
// load bam files
//polyscan.LoadBams( normalBam, tumorBam );
if (!normalBam.empty() && !tumorBam.empty()) {
polyscan.LoadBams( normalBam, tumorBam );
}
// just for tumor only data
if (normalBam.empty() && !tumorBam.empty()) {
polyscan.LoadBam(tumorBam);
}
// check h**o/microsate file
finH.open(homoFile.c_str());
if (!finH) {
std::cerr<<"fatal error: failed to open homopolymer and microsatellites file\n";
exit(1);
}
std::cout << "loading homopolymer and microsatellite sites ..." << std::endl;
polyscan.LoadHomosAndMicrosates(finH);
finH.close();
//polyscan.TestHomos();
polyscan.SplitWindows();
//polyscan.TestWindows();
std::cout << "\nTotal loading windows: " << polyscan.totalWindowsNum << " \n\n";
std::cout << "\nTotal loading homopolymer and microsatellites: " << polyscan.totalHomosites << " \n\n";
// change code to one sample
//polyscan.GetHomoDistribution(sample, disFile);
// control distribution for tumor only input
if (!normalBam.empty() && !tumorBam.empty()) {
polyscan.GetHomoDistribution(sample, disFile);
}
if (normalBam.empty() && !tumorBam.empty()) {
polyscan.GetHomoTumorDistribution(sample, disFile);
}
std::cout << "\nTotal time consumed: " << Cal_AllTime() << " secs\n\n";
return 0;
}