QString NetworkInterface::getFirstWiredDevice()
{
QString tmp;
QStringList ifs = getInterfaces();
for ( QStringList::Iterator it = ifs.begin(); it != ifs.end(); ++it )
{
// List of devices to exclude not real ethernet
QString tmpDev = *it;
if (tmpDev.indexOf("lo0") == -1
&& tmpDev.indexOf("lagg") == -1
&& tmpDev.indexOf("lo1") == -1
&& tmpDev.indexOf("lo2") == -1
&& tmpDev.indexOf("lo3") == -1
&& tmpDev.indexOf("fwe") == -1
&& tmpDev.indexOf("plip") == -1
&& tmpDev.indexOf("pfsync") == -1
&& tmpDev.indexOf("pflog") == -1
&& tmpDev.indexOf("ipfw") == -1
&& tmpDev.indexOf("tun") == -1
&& tmpDev.indexOf("usbus") == -1
&& tmpDev.indexOf("vboxnet") == -1
&& tmpDev.indexOf("wlan") == -1 )
{
NetworkInterface ifr(tmpDev);
if (! ifr.isWireless()) {
return tmpDev;
}
}
}
return tmp;
}
int main(int argc, char** argv)
{
const std::string program_name = "hts_AdapterTrimmer";
std::string app_description =
"Adapter Trimmer, trims off adapters by first overlapping paired-end reads and\n";
app_description += " trimming off overhangs which by definition are adapter sequence in standard\n";
app_description += " libraries. SE Reads are trimmed by overlapping the adapter-sequence and trimming off the overlap.";
try
{
/** Define and parse the program options
*/
namespace po = boost::program_options;
po::options_description standard = setStandardOptions();
// version|v ; help|h ; notes|N ; stats-file|L ; append-stats-file|A
po::options_description input = setInputOptions();
// read1-input|1 ; read2-input|2 ; singleend-input|U
// tab-input|T ; interleaved-input|I ; from-stdin|S
po::options_description output = setOutputOptions(program_name);
// force|F ; prefix|p ; gzip-output,g ; fastq-output|f
// tab-output|t ; interleaved-output|i ; unmapped-output|u ; to-stdout,O
po::options_description desc("Application Specific Options");
setDefaultParamsCutting(desc);
// no-orphans|n ; stranded|s ; min-length|m
setDefaultParamsOverlapping(desc);
// kmer|k ; kmer-offset|r ; max-mismatch-errorDensity|x
// check-lengths|c ; min-overlap|o
desc.add_options()
("no-fixbases,X", po::bool_switch()->default_value(false), "after trimming adapter, DO NOT use consensus sequence of paired reads, only trims adapter sequence");
desc.add_options()
("adapter-sequence,a", po::value<std::string>()->default_value("AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"), "Primer sequence to trim in SE adapter trimming, default is truseq ht primer sequence");
po::options_description cmdline_options;
cmdline_options.add(standard).add(input).add(output).add(desc);
po::variables_map vm;
try
{
po::store(po::parse_command_line(argc, argv, cmdline_options), vm); // can throw
version_or_help(program_name, app_description, cmdline_options, vm);
po::notify(vm); // throws on error, so do after help in case
std::string statsFile(vm["stats-file"].as<std::string>());
std::string prefix(vm["prefix"].as<std::string>());
AdapterCounters counters(statsFile, vm["append-stats-file"].as<bool>(), program_name, vm["notes"].as<std::string>());
std::shared_ptr<OutputWriter> pe = nullptr;
std::shared_ptr<OutputWriter> se = nullptr;
outputWriters(pe, se, vm["fastq-output"].as<bool>(), vm["tab-output"].as<bool>(), vm["interleaved-output"].as<bool>(), vm["unmapped-output"].as<bool>(), vm["force"].as<bool>(), vm["gzip-output"].as<bool>(), vm["to-stdout"].as<bool>(), prefix );
if(vm.count("read1-input")) { // paired-end reads
if (vm["read1-input"].as<std::vector<std::string> >().size() != vm["read1-input"].as<std::vector<std::string> >().size()) {
throw std::runtime_error("must have same number of input files for read1 and read2");
}
InputReader<PairedEndRead, PairedEndReadFastqImpl> ifr(vm["read1-input"].as<std::vector<std::string> >(), vm["read2-input"].as<std::vector<std::string> >());
helper_adapterTrimmer(ifr, pe, se, counters, vm["max-mismatch-errorDensity"].as<double>(), vm["max-mismatch"].as<size_t>(), vm["min-overlap"].as<size_t>(), vm["stranded"].as<bool>(), vm["min-length"].as<size_t>(), vm["check-lengths"].as<size_t>(), vm["kmer"].as<size_t>(), vm["kmer-offset"].as<size_t>(), vm["no-orphans"].as<bool>(), vm["no-fixbases"].as<bool>(), vm["adapter-sequence"].as<std::string>() );
}
if (vm.count("interleaved-input")) { // interleaved pairs
InputReader<PairedEndRead, InterReadImpl> ifr(vm["interleaved-input"].as<std::vector<std::string > >());
helper_adapterTrimmer(ifr, pe, se, counters, vm["max-mismatch-errorDensity"].as<double>(), vm["max-mismatch"].as<size_t>(), vm["min-overlap"].as<size_t>(), vm["stranded"].as<bool>(), vm["min-length"].as<size_t>(), vm["check-lengths"].as<size_t>(), vm["kmer"].as<size_t>(), vm["kmer-offset"].as<size_t>(), vm["no-orphans"].as<bool>(), vm["no-fixbases"].as<bool>(), vm["adapter-sequence"].as<std::string>() );
}
if(vm.count("singleend-input")) { // single-end reads
InputReader<SingleEndRead, SingleEndReadFastqImpl> ifr(vm["singleend-input"].as<std::vector<std::string> >());
helper_adapterTrimmer(ifr, pe, se, counters, vm["max-mismatch-errorDensity"].as<double>(), vm["max-mismatch"].as<size_t>(), vm["min-overlap"].as<size_t>(), vm["stranded"].as<bool>(), vm["min-length"].as<size_t>(), vm["check-lengths"].as<size_t>(), vm["kmer"].as<size_t>(), vm["kmer-offset"].as<size_t>(), vm["no-orphans"].as<bool>(), vm["no-fixbases"].as<bool>(), vm["adapter-sequence"].as<std::string>() );
}
if(vm.count("tab-input")) { // tab_input
InputReader<ReadBase, TabReadImpl> ifr(vm["tab-input"].as<std::vector<std::string> > ());
helper_adapterTrimmer(ifr, pe, se, counters, vm["max-mismatch-errorDensity"].as<double>(), vm["max-mismatch"].as<size_t>(), vm["min-overlap"].as<size_t>(), vm["stranded"].as<bool>(), vm["min-length"].as<size_t>(), vm["check-lengths"].as<size_t>(), vm["kmer"].as<size_t>(), vm["kmer-offset"].as<size_t>(), vm["no-orphans"].as<bool>(), vm["no-fixbases"].as<bool>(), vm["adapter-sequence"].as<std::string>() );
}
if(vm["from-stdin"].as<bool>()) { // stdin
bi::stream<bi::file_descriptor_source> tabin {fileno(stdin), bi::close_handle};
InputReader<ReadBase, TabReadImpl> ifr(tabin);
helper_adapterTrimmer(ifr, pe, se, counters, vm["max-mismatch-errorDensity"].as<double>(), vm["max-mismatch"].as<size_t>(), vm["min-overlap"].as<size_t>(), vm["stranded"].as<bool>(), vm["min-length"].as<size_t>(), vm["check-lengths"].as<size_t>(), vm["kmer"].as<size_t>(), vm["kmer-offset"].as<size_t>(), vm["no-orphans"].as<bool>(), vm["no-fixbases"].as<bool>(), vm["adapter-sequence"].as<std::string>() );
}
// no input specified on the command line
if (!vm.count("read1-input") && !vm.count("interleaved-input") && !vm.count("singleend-input") && !vm.count("tab-input") && !vm["from-stdin"].as<bool>()) {
std::cerr << "ERROR: " << "Input file type absent from command line" << std::endl << std::endl;
version_or_help(program_name, app_description, cmdline_options, vm, true);
exit(ERROR_IN_COMMAND_LINE); //success
}
counters.write_out();
}
catch(po::error& e)
{
std::cerr << "ERROR: " << e.what() << std::endl << std::endl;
return ERROR_IN_COMMAND_LINE;
}
}
catch(std::exception& e)
{
std::cerr << "\n\tUnhandled Exception: "
<< e.what() << std::endl;
return ERROR_UNHANDLED_EXCEPTION;
}
return SUCCESS;
}
