// Constructor
Input(int argc, char **argv)
: ec_(false), shortestOnly_(false), distances_(false), suppressRef_(false),
overlaps_(true), delim_("|"), refFile_(""), nonRefFile_(""), chr_("all") {
typedef Ext::UserError UE;
if ( 1 == argc )
throw(NoInput());
int argcntr = 1;
bool outoption = false; // may choose up to one type of non-default output option
// [Process-Flags]
std::string next = "";
while ( argcntr < argc ) {
next = argv[argcntr];
if ( next == "--help" )
throw(HelpException());
else if ( next == "--version" )
throw(VersionException());
else if ( next == "--ec" || next == "--header" )
ec_ = true;
else if ( next == "--no-overlaps" )
overlaps_ = false;
else if ( next == "--delim" ) {
Ext::Assert<UE>(++argcntr < argc, "No value given for --delim.");
delim_ = argv[argcntr];
}
else if ( next == "--chrom" ) {
Ext::Assert<UE>(++argcntr < argc, "No value given for --chrome.");
chr_ = argv[argcntr];
}
else if ( next == "--closest" ) {
Ext::Assert<UE>(!outoption, "Multiple output options not allowed.");
shortestOnly_ = true;
outoption = true;
}
else if ( next == "--dist" )
distances_ = true;
else if ( next == "--no-ref" )
suppressRef_ = true;
else if ( next == "--help" )
throw(HelpException());
else if ( next == "--shortest" ) { // silently supported for bckwd compatibility
Ext::Assert<UE>(!outoption, "Multiple output options not allowed.");
shortestOnly_ = true;
outoption = true;
} else { // the rest are two input files?
Ext::Assert<UE>(argcntr + 2 == argc, "Unknown option: " + next + ".");
break;
}
++argcntr;
} // while
Ext::Assert<UE>(argcntr + 2 == argc, "Not enough input files given.");
refFile_ = argv[argcntr++];
nonRefFile_ = argv[argcntr];
Ext::Assert<UE>(refFile_.find("--") != 0, "Option given where file expected: " + refFile_ + ".");
Ext::Assert<UE>(nonRefFile_.find("--") != 0, "Option given where file expected: " + nonRefFile_ + ".");
}
void CommandLineParser::parseArgs(const std::vector<StringView>& args, CommandLineFlags& result) const
{
size_t numPositionalConsumed = 0;
size_t numFlagConsumed = 0;
while (numFlagConsumed < args.size())
{
auto flag = args[numFlagConsumed];
if (!isOption(flag)) // Positional arguments
{
if (numPositionalConsumed >= posFlagMap.size())
throw ParseException("too many positional arguments");
auto inserted = result.addFlag(posFlagMap[numPositionalConsumed].first, flag);
assert(inserted && "Insertion failed");
++numPositionalConsumed;
}
else // Optional arguments
{
flag.remove_prefix(1);
// See if flag is "-help"
if (flag == "help")
throw HelpException();
auto itr = optFlagMap.find(flag);
if (itr == optFlagMap.end())
throw ParseException("Option not recognized: " + flag.to_string());
if (itr->second.defaultValue)
{
++numFlagConsumed;
if (numFlagConsumed >= args.size())
throw ParseException("More argument needs to be provided after option " + flag.to_string());
auto flagArg = args[numFlagConsumed];
if (isOption(flagArg))
throw ParseException("Found another option instead of an argument after option " + flag.to_string());
auto inserted = result.addFlag(flag, flagArg);
assert(inserted && "Insertion failed");
}
else
{
auto inserted = result.addFlag(flag, "");
assert(inserted && "Insertion failed");
}
}
++numFlagConsumed;
}
if (numPositionalConsumed < posFlagMap.size())
throw ParseException("Not enough positional arguments are provided");
for (auto const& mapping: optFlagMap)
{
if (mapping.second.defaultValue && result.lookup(mapping.first) == nullptr)
result.addFlag(mapping.first, *mapping.second.defaultValue);
}
}
/**
* Supported options are '-h', '-v'.
* @throws HelpException when only help is need
* @throws LogicException when used option is unknown
*/
void
OptionAgent::parseDashOpt(const std::string &arg,
const OptionParams ¶ms)
{
if ("-h" == arg || "--help" == arg) {
throw HelpException(ExInfo(getHelpInfo(params)));
}
else if ("-v" == arg || "--version" == arg) {
throw HelpException(ExInfo(getVersionInfo()));
}
else if ("-c" == arg || "--config" == arg) {
throw HelpException(ExInfo(params.getConfig(m_environ)));
}
else {
throw LogicException(ExInfo("unknown option")
.addInfo("arg", arg)
.addInfo("use",
getParam("program") + " --help"));
}
}
