string SimulateRead(const SequencingParameters& p,
const std::string& tpl,
RandomNumberGenerator& rng)
{
std::string read;
read.reserve(tpl.length() * 2);
int pos = 0;
while (pos < (int)tpl.length())
{
char base = tpl[pos];
char prevBase = pos > 0 ? tpl[pos-1] : 'N';
int channel = Channel(base);
//
// Tabulate the different possible move probabilities, then choose one
//
bool canMerge = base == prevBase;
vector<double> errorProbs = ErrorProbs(p, channel, canMerge);
int choice = rng.RandomChoice(errorProbs);
if (choice == (int) errorProbs.size() - 1) { // Match
read.push_back(base);
pos++;
} else if (choice < 4) { // Insert
vector<double> insertProbs = vector<double>(errorProbs.begin(),
errorProbs.begin() + 4);
int eChannel = rng.RandomChoice(insertProbs);
char eBase = "TGAC"[eChannel];
read.push_back(eBase);
} else if (choice == 4) { // Dark
pos++;
} else if (choice == 5) { // Miscall
read.push_back(rng.RandomBase());
pos++;
} else { // Merge
assert (canMerge);
pos++;
}
}
return read;
}
