...
 
Commits (2)
......@@ -258,14 +258,14 @@ main(int argc, char const *argv[])
std::string radiantVersion(std::string(STR(MAJOR_VERSION)) + "." + std::string(STR(MINOR_VERSION)) + "." + std::string(STR(PATCH_VERSION)) );
try
{
std::string in_string, out_string;
fs::path inFile, databaseFile;
//int nThreads;
po::options_description allOpts("radiant " + radiantVersion + " (C) 2017 Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
po::options_description general("General options");
general.add_options()
("help,h", "Produces this help message")
("in,i", po::value<fs::path>(&inFile)->required()->value_name("FILE"), "The input file")
("in,i", po::value<std::string>(&in_string)->required()->value_name("FILE"), "The input file")
("database,d", po::value<fs::path>(&databaseFile)->required()->value_name("DIRECTORY"), "The path to the database")
//("nThreads,t", po::value<int>(&nThreads)->default_value(1), "Number of threads to use")
;
......@@ -274,7 +274,7 @@ main(int argc, char const *argv[])
bool pfamLike, noHeader;
po::options_description outputO("Output options");
outputO.add_options()
("out,o", po::value<fs::path>(&outFile)->value_name("FILE"), "The output file")
("out,o", po::value<std::string>(&out_string)->value_name("FILE"), "The output file")
("pfam-like,p", po::value<bool>(&pfamLike)->default_value(false)->zero_tokens(), "Produces a fake Pfam format")
("no-header,n", po::value<bool>(&noHeader)->default_value(false)->zero_tokens(), "Do not print the header")
;
......@@ -300,6 +300,7 @@ main(int argc, char const *argv[])
po::options_description visible("radiant " + radiantVersion + " (C) 2017,2018 Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
visible.add(general).add(outputO).add(translateO);
try
{
po::variables_map vm;
......@@ -310,6 +311,7 @@ main(int argc, char const *argv[])
return EXIT_SUCCESS;
}
po::notify(vm);
}
catch (boost::program_options::error &e)
{
......@@ -319,6 +321,9 @@ main(int argc, char const *argv[])
return EXIT_FAILURE;
}
inFile = in_string;
outFile = out_string;
//omp_set_num_threads(nThreads);
BSDL::SequenceSet<BSDL::Sequence<> > seqSet;
seqSet.read(inFile);
......