int dGetOptions(int rgc, char *rgv[]) {
int i;
for (i=1; i<rgc; i++) {
if (rgv[i][0] != '-') return i;
switch(rgv[i][1]) {
case 'd': homoFile = rgv[++i]; break;
case 'n': normalBam = rgv[++i]; break;
case 't': tumorBam = rgv[++i]; break;
case 'o': disFile = rgv[++i]; break;
case 'e': bedFile = rgv[++i]; break;
case 'r': one_region = rgv[++i]; break;
case 'f': paramd.fdrThreshold = atof(rgv[++i]); break;
case 'i': paramd.comentropyThreshold = atof(rgv[++i]); break;
case 'c': paramd.covCutoff = atoi(rgv[++i]); break;
case 'z': paramd.Normalization = atoi(rgv[++i]); break;
case 'l': paramd.MininalHomoSize = atoi(rgv[++i]); break;
case 'p': paramd.MininalHomoForDis = atoi(rgv[++i]); break;
case 'u': paramd.DisSpan = atoi(rgv[++i]); break;
case 'm': paramd.MaxHomoSize = atoi(rgv[++i]); break;
case 'q': paramd.MinMicrosate = atoi(rgv[++i]); break;
case 's': paramd.MinMicrosateForDis = atoi(rgv[++i]); break;
case 'w': paramd.MaxMicrosateForDis = atoi(rgv[++i]); break;
case 'b': paramd.numberThreads = atoi(rgv[++i]); break;
case 'x': paramd.HomoOnly= atoi(rgv[++i]); break;
case 'y': paramd.MicrosateOnly = atoi(rgv[++i]); break;
break;
case 'h':DisUsage();
case '?':DisUsage();
}
}
return i;
}
int dGetOptions(int rgc, char *rgv[]) {
int i;
for (i=1; i<rgc; i++) {
if (rgv[i][0] != '-') return i;
switch(rgv[i][1]) {
case 'd': homoFile = rgv[++i]; break;
case 'b': bamListFile = rgv[++i]; break;
case 'o': disFile = rgv[++i]; break;
case 'e': bedFile = rgv[++i]; break;
case 'r': one_region = rgv[++i]; break;
case 'l': paramd.MininalHomoSize = atoi(rgv[++i]); break;
case 'p': paramd.MininalHomoForDis = atoi(rgv[++i]); break;
case 'u': paramd.DisSpan = atoi(rgv[++i]); break;
case 'm': paramd.MaxHomoSize = atoi(rgv[++i]); break;
case 'q': paramd.MinMicrosate = atoi(rgv[++i]); break;
case 's': paramd.MinMicrosateForDis = atoi(rgv[++i]); break;
case 'w': paramd.MaxMicrosateForDis = atoi(rgv[++i]); break;
case 't': paramd.numberThreads = atoi(rgv[++i]); break;
case 'x': paramd.HomoOnly= atoi(rgv[++i]); break;
case 'y': paramd.MicrosateOnly = atoi(rgv[++i]); break;
break;
case 'h':DisUsage();
case '?':DisUsage();
}
}
return i;
}
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;
}
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;
}
