int simulateGenome(char const * filename, MasonSimulateGenomeOptions const & options)
{
seqan::SequenceStream stream;
open(stream, filename, seqan::SequenceStream::WRITE, seqan::SequenceStream::FASTA);
if (!isGood(stream))
{
std::cerr << "ERROR: Could not open " << filename << "for writing!\n";
return 1;
}
return simulateGenome(stream, options);
}
int main(int argc, char const ** argv)
{
// Parse the command line.
seqan::ArgumentParser parser;
MasonGenomeOptions options;
seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
if (res != seqan::ArgumentParser::PARSE_OK)
return res == seqan::ArgumentParser::PARSE_ERROR;
std::cout << "MASON GENOME SIMULATOR\n"
<< "======================\n\n";
// Print the command line arguments back to the user.
if (options.verbosity > 0)
{
std::cout << "__OPTIONS____________________________________________________________________\n"
<< '\n'
<< "VERBOSITY \t" << options.verbosity << '\n'
<< "\n"
<< "SEED \t" << options.seed << '\n'
<< "\n"
<< "OUTPUT FILE\t" << options.outputFilename << "\n"
<< "CONTIG LENS\t";
for (unsigned i = 0; i < length(options.contigLengths); ++i)
{
if (i > 0)
std::cout << ", ";
std::cout << options.contigLengths[i];
};
std::cout << "\n\n";
}
// Perform genome simulation.
std::cout << "__SIMULATING GENOME__________________________________________________________\n"
<< "\n";
MasonSimulateGenomeOptions simOptions;
simOptions.contigLengths = options.contigLengths;
simOptions.seed = options.seed;
if (simulateGenome(toCString(options.outputFilename), simOptions) != 0)
return 1;
std::cerr << "\nDone.\n";
return 0;
}
