void update_highway_and_river ()
{
// Update the offsets of the logs and traffic patterns
int i;
for (i = 0; i < N_ELEMENTS; i ++){
//update pattern of logs [7 + i]
update_pattern(&logs[i]);
//update pattern of traffic [1 + i]
update_pattern(&traffic[i]);
}
draw_logs();
draw_traffic();
}
//
// Handle command line arguments
//
void parseScanOptions(int argc, char** argv)
{
std::string bamlistfile = "";
std::string rev = "";
Headers hd;
for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
{
std::istringstream arg(optarg != NULL ? optarg : "");
switch (c)
{
case 'f':
arg >> bamlistfile; break;
case 'o':
arg >> opt::outputfile; break;
case 'H':
opt::writerheader=false; break;
case 'm':
opt::mergerg = true; break;
case 'u':
opt::ignorerg = true; break;
case 'w':
opt::onebam = true; break;
case 'h':
for(size_t h=0; h<hd.headers.size();h++){
std::cout << hd.headers[h] << ScanParameters::FIELD_SEP;
}
std::cout << "\n";
exit(EXIT_SUCCESS);
case 'k':
arg >> opt::tel_k;
break;
case 'r':
arg >> ScanParameters::READ_LENGTH;
if(ScanParameters::READ_LENGTH <= 0 || ScanParameters::READ_LENGTH > 100000){
std::cerr << "please specify valid read length that is greater than 0 and length than 100kb" << "\n";
exit(EXIT_FAILURE);
}
break;
case 'p':
break;
case 'z':
arg >> ScanParameters::PATTERN;
ScanParameters::PATTERN_REVCOMP = reverseComplement(ScanParameters::PATTERN);
std::cerr << "use user specified pattern " << ScanParameters::PATTERN << "\n";
std::cerr << "reverse complement " << ScanParameters::PATTERN_REVCOMP << "\n";
break;
case 'e':
arg >> opt::exomebedfile;
opt::exomebed = readBedAsVector(opt::exomebedfile);
std::cout << "loaded "<< opt::exomebed.size() << " exome regions \n"<< std::endl;
// std::cout << opt::exomebed << "\n";
break;
case OPT_HELP:
std::cout << TELSEQ_USAGE_MESSAGE;
exit(EXIT_SUCCESS);
case OPT_VERSION:
std::cout << TELSEQ_VERSION_MESSAGE;
exit(EXIT_SUCCESS);
}
}
update_pattern();
// deal with cases of API usage:
// telseq a.bam b.bam c.bam ...
// | telseq
// telseq -f
if (argc - optind < 1) // no argument specified
{
// check if it is from pipe
if(!isatty(fileno(stdin))){
std::string line;
while (std::getline(std::cin, line))
{
if(line.empty()){
continue;
}
opt::bamlist.push_back(line);
}
}else if(bamlistfile.empty() ){ // check if not from a pipe, -f must be spceified
// std::cerr << SUBPROGRAM ": No BAM specified. Please specify BAM either directly, by using -f option or piping BAM file path.\n";
std::cout << TELSEQ_USAGE_MESSAGE;
exit(EXIT_FAILURE);
}
}
else if (argc - optind >= 1) // if arguments are specified
{
// -f has higher priority, when specified, ignore arguments.
if(bamlistfile.empty()){
for(int i = optind; i < argc; ++i ){
opt::bamlist.push_back(argv[i]);
}
}
}
// read in bamlist
if(!bamlistfile.empty()){
size_t filesize = getFilesize(bamlistfile);
if(filesize == 0)
{
std::cerr << PROGRAM_BIN ": BAMLIST file specified by -f is empty\n";
exit(EXIT_FAILURE);
}
std::istream* pReader = createReader(bamlistfile);
std::string line;
while(getline(*pReader, line))
{
if(line.empty()){
continue;
}
opt::bamlist.push_back(line);
}
size_t bamsize = opt::bamlist.size();
if(bamsize == 0 ){
std::cerr << PROGRAM_BIN ": Could find any sample in BAMLIST file specified.\n";
exit(EXIT_FAILURE);
}
delete pReader;
}
// check output
// for(size_t i = 0; i < opt::bamlist.size(); ++i ){
// std::cerr << "opt::bamlist:" << opt::bamlist[i] << "\n";
// }
// std::cerr << "opt::bamlistfile:" << bamlistfile << "\n";
// std::cerr << "opt::writerheader:" << opt::writerheader << "\n";
// std::cerr << "opt::tel_k:" << opt::tel_k << "\n";
// std::cerr << "opt::outputdir:" << opt::outputfile << "\n";
}