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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>
// ==========================================================================
#include "sequencing.h"
// Maximal homopolymer length we will observe.
const unsigned MAX_HOMOPOLYMER_LEN = 40;
// ---------------------------------------------------------------------------
// Constructor Roche454SequencingSimulator::Roche454SequencingSimulator()
// ---------------------------------------------------------------------------
Roche454SequencingSimulator::Roche454SequencingSimulator(
TRng & rng,
TRng & methRng,
SequencingOptions const & seqOptions,
Roche454SequencingOptions const & roche454Options) :
SequencingSimulator(rng, methRng, seqOptions), roche454Options(roche454Options), model(new Roche454Model())
{
_initModel();
}
// ---------------------------------------------------------------------------
// Function Roche454SequencingSimulator::_initModel()
// ---------------------------------------------------------------------------
// Initialize the threshold matrix.
void Roche454SequencingSimulator::_initModel()
{
model->thresholdMatrix.setK(roche454Options.k);
model->thresholdMatrix.setUseSqrt(roche454Options.sqrtInStdDev);
model->thresholdMatrix.setNoiseMeanStdDev(roche454Options.backgroundNoiseMean, roche454Options.backgroundNoiseStdDev);
}
// ---------------------------------------------------------------------------
// Function Roche454SequencingSimulator::readLength()
// ---------------------------------------------------------------------------
unsigned Roche454SequencingSimulator::readLength()
{
if (roche454Options.lengthModel == Roche454SequencingOptions::UNIFORM)
{
// Pick uniformly.
double minLen = roche454Options.minReadLength;
double maxLen = roche454Options.maxReadLength;
std::uniform_real_distribution<double> dist(minLen, maxLen);
double len = dist(rng);
return static_cast<unsigned>(round(len));
}
else
{
// Pick normally distributed.
std::normal_distribution<double> dist(roche454Options.meanReadLength,
roche454Options.stdDevReadLength);
double len = dist(rng);
return static_cast<unsigned>(round(len));
}
}
// ---------------------------------------------------------------------------
// Function Roche454SequencingSimulator::simulateRead()
// ---------------------------------------------------------------------------
void Roche454SequencingSimulator::simulateRead(
TRead & seq, TQualities & quals, SequencingSimulationInfo & info,
TFragment const & frag, Direction dir, Strand strand)
{
clear(seq);
clear(quals);
// Compute read length and check whether it fits in fragment.
unsigned sampleLength = this->readLength();
if (sampleLength > length(frag))
{
throw std::runtime_error("454 read is too long, increase fragment length");
}
// Get a copy of the to be sequenced base stretch.
TRead haplotypeInfix;
if (dir == LEFT)
haplotypeInfix = prefix(frag, sampleLength);
else
haplotypeInfix = suffix(frag, length(frag) - sampleLength);
if (strand == REVERSE)
reverseComplement(haplotypeInfix);
// In the flow cell simulation, we will simulate light intensities which will be stored in observedIntensities.
seqan2::String<double> observedIntensities;
reserve(observedIntensities, 4 * sampleLength);
seqan2::Dna5String observedBases;
// We also store the real homopolymer length.
seqan2::String<unsigned> realBaseCount;
// Probability density function to use for the background noise.
std::lognormal_distribution<double> distNoise(seqan2::cvtLogNormalDistParam(roche454Options.backgroundNoiseMean,
roche454Options.backgroundNoiseStdDev));
// Initialize information about the current homopolymer length.
unsigned homopolymerLength = 0;
seqan2::Dna homopolymerType = haplotypeInfix[0];
while (homopolymerLength < length(haplotypeInfix) && haplotypeInfix[homopolymerLength] == homopolymerType)
++homopolymerLength;
// Simulate flowcell.
for (unsigned i = 0, j = 0; i < sampleLength; ++j, j = j % 4) // i indicates first pos of current homopolymer, j indicates flow phase
{
if (ordValue(homopolymerType) == j)
{
// Simulate positive flow observation.
double l = homopolymerLength;
double sigma = roche454Options.k * (roche454Options.sqrtInStdDev ? sqrt(l) : l);
std::normal_distribution<double> distIntensity(homopolymerLength, sigma);
double intensity = distIntensity(rng);
intensity += distNoise(rng); // Add noise.
appendValue(observedIntensities, intensity);
appendValue(realBaseCount, homopolymerLength);
// Get begin pos and length of next homopolymer.
i += homopolymerLength;
if (i < length(haplotypeInfix))
{
homopolymerType = haplotypeInfix[i];
homopolymerLength = 0;
while (((i + homopolymerLength) < length(haplotypeInfix)) && haplotypeInfix[i + homopolymerLength] == homopolymerType)
++homopolymerLength;
}
}
else
{
// Simulate negative flow observation.
//
// Constants taken from MetaSim paper which have it from the
// original 454 publication.
double intensity = std::max(0.0, distNoise(rng));
appendValue(observedIntensities, intensity);
appendValue(realBaseCount, 0);
}
}
seqan2::String<seqan2::CigarElement<> > cigar;
// Call bases, from this build the edit string and maybe qualities. We only support the "inter" base calling
// method which was published by the MetaSim authors in the PLOS paper.
typedef seqan2::Iterator<seqan2::String<double>, seqan2::Standard>::Type IntensitiesIterator;
int i = 0; // Flow round, Dna(i % 4) gives base.
for (IntensitiesIterator it = begin(observedIntensities); it != end(observedIntensities); ++it, ++i)
{
double threshold = model->thresholdMatrix.getThreshold(static_cast<unsigned>(floor(*it)), static_cast<unsigned>(ceil(*it)));
unsigned calledBaseCount = static_cast<unsigned>(*it < threshold ? floor(*it) : ceil(*it));
// Add any matches.
unsigned j = 0;
for (; j < std::min(calledBaseCount, realBaseCount[i]); ++j)
{
appendOperation(cigar, 'M');
appendValue(seq, seqan2::Dna(i % 4));
}
// Add insertions, if any.
for (; j < calledBaseCount; ++j)
{
appendOperation(cigar, 'I');
appendValue(seq, seqan2::Dna(i % 4));
}
// Add deletions, if any.
for (; j < realBaseCount[i]; ++j)
appendOperation(cigar, 'D');
// Simulate qualities if configured to do so.
if (seqOptions->simulateQualities)
{
// Compute likelihood for calling the bases, given this intensity and the Phred score from this.
double densitySum = 0;
for (unsigned j = 0; j <= std::max(4u, 2 * MAX_HOMOPOLYMER_LEN); ++j) // Anecdotally through plot in maple: Enough to sum up to 4 or 2 times the maximal homopolymer length.
densitySum += model->thresholdMatrix.dispatchDensityFunction(j, *it);
double x = 0; // Probability of seeing < (j+1) bases.
for (unsigned j = 0; j < calledBaseCount; ++j) {
x += model->thresholdMatrix.dispatchDensityFunction(j, *it);
int q = -static_cast<int>(10 * ::std::log10(x / densitySum));
q = std::max(0, std::min(40, q));
appendValue(quals, (char)('!' + q));
}
}
}
// Write out extended sequencing information info if configured to do so. We always write out the sample position
// and alignment information.
info.cigar = cigar;
unsigned len = 0;
_getLengthInRef(len, cigar);
info.beginPos = (dir == LEFT) ? beginPosition(frag) : (beginPosition(frag) + length(frag) - len);
info.isForward = (strand == FORWARD);
if (seqOptions->embedReadInfo)
{
if (dir == LEFT)
info.sampleSequence = prefix(frag, len);
else
info.sampleSequence = suffix(frag, length(frag) - len);
if (strand == REVERSE)
reverseComplement(info.sampleSequence);
}
}
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