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// ==========================================================================
// Mason - A Read Simulator
// ==========================================================================
// Copyright (c) 2006-2026, 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>
// ==========================================================================
// Simulate a random genome.
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>
#include <seqan/arg_parse.h>
#include "mason_options.h"
#include "methylation_levels.h"
// ==========================================================================
// Classes
// ==========================================================================
// ==========================================================================
// Functions
// ==========================================================================
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
seqan2::ArgumentParser::ParseResult
parseCommandLine(MasonMethylationOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
seqan2::ArgumentParser parser("mason_methylation");
// Set short description, version, and date.
setShortDescription(parser, "Methylation Level Simulation");
setDateAndVersion(parser);
setCategory(parser, "Simulators");
// Define usage line and long description.
addUsageLine(parser, "[OPTIONS] \\fB-i\\fP \\fIIN.fa\\fP \\fB-o\\fP \\fIOUT.fa\\fP");
addDescription(parser, "Simulate methylation levels for \\fIIN.fa\\fP and write them to \\fIOUT.fa\\fP.");
options.addOptions(parser);
// Parse command line.
seqan2::ArgumentParser::ParseResult res = seqan2::parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != seqan2::ArgumentParser::PARSE_OK)
return res;
options.getOptionValues(parser);
options.methOptions.simulateMethylationLevels = true;
return seqan2::ArgumentParser::PARSE_OK;
}
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
MasonMethylationOptions options;
seqan2::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 != seqan2::ArgumentParser::PARSE_OK)
return res == seqan2::ArgumentParser::PARSE_ERROR;
std::cerr << "MASON METHYLATION SIMULATION\n"
<< "============================\n\n";
// Print the command line arguments back to the user.
if (options.verbosity > 0)
options.print(std::cerr);
std::cerr << "\n__PREPARATION_________________________________________________________________\n"
<< "\n";
std::cerr << "Loading Reference Index " << options.fastaInFile << " ...";
seqan2::FaiIndex faiIndex;
if (!open(faiIndex, toCString(options.fastaInFile)))
{
std::cerr << " FAILED (not fatal, we can just build it)\n";
std::cerr << "Building Index " << options.fastaInFile << ".fai ...";
if (!build(faiIndex, toCString(options.fastaInFile)))
{
std::cerr << "Could not build FAI index.\n";
return 1;
}
std::cerr << " OK\n";
seqan2::CharString faiPath = options.fastaInFile;
append(faiPath, ".fai");
std::cerr << "Reference Index " << faiPath << " ...";
if (!save(faiIndex, toCString(faiPath)))
{
std::cerr << "Could not write FAI index we just built.\n";
return 1;
}
std::cerr << " OK (" << length(faiIndex.indexEntryStore) << " seqs)\n";
}
else
{
std::cerr << " OK (" << length(faiIndex.indexEntryStore) << " seqs)\n";
}
std::cerr << "Opening output File " << options.methFastaOutFile << " ...";
seqan2::SeqFileOut outStream;
if (!open(outStream, toCString(options.methFastaOutFile)))
{
std::cerr << "\nERROR: Could not open output file.\n";
return 1;
}
std::cerr << " OK\n";
std::cerr << "\n__SIMULATION__________________________________________________________________\n"
<< "\n";
TRng rng(options.seed);
MethylationLevelSimulator methSim(rng, options.methOptions);
MethylationLevels levels;
seqan2::Dna5String contig;
for (unsigned i = 0; i < numSeqs(faiIndex); ++i)
{
levels.clear();
std::cerr << "Simulating for " << sequenceName(faiIndex, i) << " ...";
readSequence(contig, faiIndex, i);
methSim.run(levels, contig);
std::stringstream ssTop;
ssTop << sequenceName(faiIndex, i) << "/TOP";
writeRecord(outStream, ssTop.str().c_str(), levels.forward);
std::stringstream ssBottom;
ssBottom << sequenceName(faiIndex, i) << "/BOT";
writeRecord(outStream, ssBottom.str().c_str(), levels.reverse);
std::cerr << " OK\n";
}
std::cerr << "\nDone with methylation simulation.\n";
return 0;
}
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