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// ==========================================================================
// SeqCons
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
#include <stdexcept>
#include <seqan/arg_parse.h>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include "seqcons_app.h"
#include "seqcons_options.h"
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
seqan::ArgumentParser parser;
SeqConsOptions 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;
// Print the command line arguments back to the user.
if (options.verbosity >= 1)
{
std::cerr << "SeqCons\n"
<< "=======\n"
<< "\n"
<< "__OPTIONS____________________________________________________________________\n"
<< '\n';
options.print(std::cerr);
}
// Perform additional consistency checking of options.
try
{
options.checkConsistency();
}
catch (std::runtime_error & e)
{
std::cerr << "\nERROR: Inconsistent command line options:\n"
<< " " << e.what() << "\n";
return 1;
}
// Run aplication.
double startTime = seqan::sysTime();
try
{
SeqConsApp app(options);
app.run();
}
catch (std::runtime_error & e)
{
std::cerr << "\nERROR: An error occurred during the program's execution:\n"
<< " " << e.what() << "\n";
return 1;
}
if (options.verbosity >= 1)
{
std::cerr << "\nOverall time: " << seqan::sysTime() - startTime << " s\n"
<< "\n"
<< "Done. Have a nice day.\n";
}
return 0;
}
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