// Simulate single-end sequencing from a fragment.
void SequencingSimulator::_simulateBSTreatment(seqan::Dna5String & methFragment,
TFragment const & frag,
MethylationLevels const & levels,
bool reverse)
{
methFragment = frag;
for (unsigned pos = 0; pos != length(frag); ++pos)
{
double level = reverse ? levels.levelR(pos + beginPosition(frag)) : levels.levelF(pos + beginPosition(frag));
if ((!reverse && methFragment[pos] != 'C') || (reverse && methFragment[pos] != 'G')) // Skip all non-cyteline chars
{
SEQAN_ASSERT_EQ_MSG(level, 0.0,
"Methylation for non-C should be 0 (pos+beginPosition(frag)=%d, reverse=%u",
pos + beginPosition(frag), reverse);
continue;
}
// Decide whether methFragment[pos] is methylated. If this is the case then we leave it untouched.
seqan::Pdf<seqan::Uniform<double> > pdf(0, 1);
if (pickRandomNumber(methRng, pdf) < level)
continue;
// Otherwise, pick whether we will convert.
if (pickRandomNumber(methRng, pdf) < seqOptions->bsSeqOptions.bsConversionRate)
methFragment[pos] = reverse ? 'A' : 'T';
}
}
// Simulate single-end sequencing from a fragment.
void SequencingSimulator::simulateSingleEnd(TRead & seq, TQualities & quals, SequencingSimulationInfo & info,
TFragment const & frag,
MethylationLevels const * levels)
{
bool isForward;
if (seqOptions->strands == SequencingOptions::BOTH)
isForward = (pickRandomNumber(rng, seqan::Pdf<seqan::Uniform<int> >(0, 1)) == 1);
else
isForward = (seqOptions->strands == SequencingOptions::FORWARD);
if (!seqOptions->bsSeqOptions.bsSimEnabled)
{
_simulateSingleEnd(seq, quals, info, frag, isForward);
}
else
{
SEQAN_ASSERT(levels);
bool bsForward = isForward;
// Re-pick strandedness of the BS-treated fragment.
if (seqOptions->bsSeqOptions.bsProtocol != BSSeqOptions::DIRECTIONAL)
bsForward = (pickRandomNumber(methRng, seqan::Pdf<seqan::Uniform<int> >(0, 1)) == 1);
_simulateBSTreatment(methFrag, frag, *levels, !bsForward);
_simulateSingleEnd(seq, quals, info, infix(methFrag, 0, length(methFrag)), isForward);
}
}
int simulateGenome(seqan::SequenceStream & stream, MasonSimulateGenomeOptions const & options)
{
// Initialize RNG and PDF.
seqan::Rng<seqan::MersenneTwister> rng(options.seed);
seqan::Pdf<seqan::Uniform<double> > pdf(0, 1);
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 = pickRandomNumber(rng, pdf);
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;
}
if (writeRecord(stream, id, contig) != 0)
{
std::cerr << "\nERROR: Could not write contig " << id << " to output file.\n";
return 1;
}
std::cerr << " DONE\n";
}
return 0;
}
