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// ==========================================================================
// Mason - A Read Simulator
// ==========================================================================
// Copyright (c) 2006-2016, 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 "simulate_genome.h"
#include <random>
// ----------------------------------------------------------------------------
// Function simulateGenome()
// ----------------------------------------------------------------------------
// Simulate a genome given the simulation options.
//
// The resulting sequence is written to stream.
int simulateGenome(seqan::SeqFileOut & stream, MasonSimulateGenomeOptions const & options)
{
// Initialize std generator and distribution
std::mt19937 generator(42); // seed 100
std::uniform_real_distribution<double> distribution(0, 1);
auto randomNumber = std::bind ( distribution, generator );
seqan::CharString id;
seqan::Dna5String contig;
for (unsigned i = 0; i < length(options.contigLengths); ++i)
{
clear(id);
clear(contig);
std::stringstream ss;
ss << (i + 1);
id = ss.str();
std::cerr << "contig " << id << " ...";
for (int j = 0; j < options.contigLengths[i];)
{
double x = randomNumber();
if (x < 0.25)
appendValue(contig, 'A');
else if (x < 0.5)
appendValue(contig, 'C');
else if (x < 0.75)
appendValue(contig, 'G');
else if (x < 1.0)
appendValue(contig, 'T');
else
continue; // Redraw.
++j;
}
try
{
writeRecord(stream, id, contig);
}
catch (seqan::IOError const & ioErr)
{
std::cerr << "\nERROR: Could not write contig " << id << " to output file.\n";
return 1;
}
std::cerr << " DONE\n";
}
return 0;
}
// ----------------------------------------------------------------------------
// Function simulateGenome()
// ----------------------------------------------------------------------------
int simulateGenome(char const * filename, MasonSimulateGenomeOptions const & options)
{
seqan::SeqFileOut stream;
if (!open(stream, filename))
{
std::cerr << "ERROR: Could not open " << filename << "for writing!\n";
return 1;
}
return simulateGenome(stream, options);
}
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