RcppExport SEXP treePhaser(SEXP Rsignal, SEXP RkeyFlow, SEXP RflowCycle, SEXP Rcf, SEXP Rie, SEXP Rdr, SEXP Rbasecaller)
{
SEXP ret = R_NilValue;
char *exceptionMesg = NULL;
try {
RcppMatrix<double> signal(Rsignal);
RcppVector<int> keyFlow(RkeyFlow);
string flowCycle = Rcpp::as<string>(RflowCycle);
double cf = Rcpp::as<double>(Rcf);
double ie = Rcpp::as<double>(Rie);
double dr = Rcpp::as<double>(Rdr);
string basecaller = Rcpp::as<string>(Rbasecaller);
unsigned int nFlow = signal.cols();
unsigned int nRead = signal.rows();
if(basecaller != "treephaser-swan" && basecaller != "dp-treephaser" && basecaller != "treephaser-adaptive") {
std::string exception = "base value for basecaller supplied: " + basecaller;
exceptionMesg = copyMessageToR(exception.c_str());
} else if (flowCycle.length() < nFlow) {
std::string exception = "Flow cycle is shorter than number of flows to solve";
exceptionMesg = copyMessageToR(exception.c_str());
} else {
// Prepare objects for holding and passing back results
RcppMatrix<double> predicted_out(nRead,nFlow);
RcppMatrix<double> residual_out(nRead,nFlow);
RcppMatrix<int> hpFlow_out(nRead,nFlow);
std::vector< std::string> seq_out(nRead);
// Set up key flow vector
int nKeyFlow = keyFlow.size();
vector <int> keyVec(nKeyFlow);
for(int iFlow=0; iFlow < nKeyFlow; iFlow++)
keyVec[iFlow] = keyFlow(iFlow);
// Iterate over all reads
vector <float> sigVec(nFlow);
string result;
for(unsigned int iRead=0; iRead < nRead; iRead++) {
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++)
sigVec[iFlow] = (float) signal(iRead,iFlow);
BasecallerRead read;
read.SetDataAndKeyNormalize(&(sigVec[0]), (int)nFlow, &(keyVec[0]), nKeyFlow-1);
DPTreephaser dpTreephaser(flowCycle.c_str(), flowCycle.length(), 8);
if (basecaller == "dp-treephaser")
dpTreephaser.SetModelParameters(cf, ie, dr);
else
dpTreephaser.SetModelParameters(cf, ie, 0); // Adaptive normalization
// Execute the iterative solving-normalization routine
if (basecaller == "dp-treephaser")
dpTreephaser.NormalizeAndSolve4(read, nFlow);
else if (basecaller == "treephaser-adaptive")
dpTreephaser.NormalizeAndSolve3(read, nFlow); // Adaptive normalization
else
dpTreephaser.NormalizeAndSolve5(read, nFlow); // sliding window adaptive normalization
read.flowToString(flowCycle,seq_out[iRead]);
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++) {
predicted_out(iRead,iFlow) = (double) read.prediction[iFlow];
residual_out(iRead,iFlow) = (double) read.normalizedMeasurements[iFlow] - read.prediction[iFlow];
hpFlow_out(iRead,iFlow) = (int) read.solution[iFlow];
}
// Store results
RcppResultSet rs;
rs.add("seq", seq_out);
rs.add("predicted", predicted_out);
rs.add("residual", residual_out);
rs.add("hpFlow", hpFlow_out);
ret = rs.getReturnList();
}
}
} catch(std::exception& ex) {
exceptionMesg = copyMessageToR(ex.what());
} catch(...) {
exceptionMesg = copyMessageToR("unknown reason");
}
if(exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}
RcppExport SEXP treePhaser(SEXP Rsignal, SEXP RkeyFlow, SEXP RflowCycle,
SEXP Rcf, SEXP Rie, SEXP Rdr, SEXP Rbasecaller, SEXP RdiagonalStates,
SEXP RmodelFile, SEXP RmodelThreshold, SEXP Rxval, SEXP Ryval)
{
SEXP ret = R_NilValue;
char *exceptionMesg = NULL;
try {
Rcpp::NumericMatrix signal(Rsignal);
Rcpp::IntegerVector keyFlow(RkeyFlow);
string flowCycle = Rcpp::as<string>(RflowCycle);
Rcpp::NumericVector cf_vec(Rcf);
Rcpp::NumericVector ie_vec(Rie);
Rcpp::NumericVector dr_vec(Rdr);
string basecaller = Rcpp::as<string>(Rbasecaller);
unsigned int diagonalStates = Rcpp::as<int>(RdiagonalStates);
// Recalibration Variables
string model_file = Rcpp::as<string>(RmodelFile);
int model_threshold = Rcpp::as<int>(RmodelThreshold);
Rcpp::IntegerVector x_values(Rxval);
Rcpp::IntegerVector y_values(Ryval);
RecalibrationModel recalModel;
if (model_file.length() > 0) {
recalModel.InitializeModel(model_file, model_threshold);
}
ion::FlowOrder flow_order(flowCycle, flowCycle.length());
unsigned int nFlow = signal.cols();
unsigned int nRead = signal.rows();
if(basecaller != "treephaser-swan" && basecaller != "treephaser-solve" && basecaller != "dp-treephaser" && basecaller != "treephaser-adaptive") {
std::string exception = "base value for basecaller supplied: " + basecaller;
exceptionMesg = strdup(exception.c_str());
} else if (flowCycle.length() < nFlow) {
std::string exception = "Flow cycle is shorter than number of flows to solve";
exceptionMesg = strdup(exception.c_str());
} else {
// Prepare objects for holding and passing back results
Rcpp::NumericMatrix predicted_out(nRead,nFlow);
Rcpp::NumericMatrix residual_out(nRead,nFlow);
Rcpp::NumericMatrix norm_additive_out(nRead,nFlow);
Rcpp::NumericMatrix norm_multipl_out(nRead,nFlow);
std::vector< std::string> seq_out(nRead);
// Set up key flow vector
int nKeyFlow = keyFlow.size();
vector <int> keyVec(nKeyFlow);
for(int iFlow=0; iFlow < nKeyFlow; iFlow++)
keyVec[iFlow] = keyFlow(iFlow);
// Iterate over all reads
vector <float> sigVec(nFlow);
BasecallerRead read;
DPTreephaser dpTreephaser(flow_order);
dpTreephaser.SetStateProgression((diagonalStates>0));
// In contrast to pipeline, we always use droop here.
// To have the same behavior of treephaser-swan as in the pipeline, supply dr=0
bool per_read_phasing = true;
if (cf_vec.size() == 1) {
per_read_phasing = false;
dpTreephaser.SetModelParameters((double)cf_vec(0), (double)ie_vec(0), (double)dr_vec(0));
}
// Main loop iterating over reads and solving them
for(unsigned int iRead=0; iRead < nRead; iRead++) {
// Set phasing parameters for this read
if (per_read_phasing)
dpTreephaser.SetModelParameters((double)cf_vec(iRead), (double)ie_vec(iRead), (double)dr_vec(iRead));
// And load recalibration model
if (recalModel.is_enabled()) {
int my_x = (int)x_values(iRead);
int my_y = (int)y_values(iRead);
const vector<vector<vector<float> > > * aPtr = 0;
const vector<vector<vector<float> > > * bPtr = 0;
aPtr = recalModel.getAs(my_x, my_y);
bPtr = recalModel.getBs(my_x, my_y);
if (aPtr == 0 or bPtr == 0) {
cout << "Error finding a recalibration model for x: " << x_values(iRead) << " y: " << y_values(iRead);
cout << endl;
}
dpTreephaser.SetAsBs(aPtr, bPtr);
}
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++)
sigVec[iFlow] = (float) signal(iRead,iFlow);
// Interface to just solve without any normalization
if (basecaller == "treephaser-solve") { // Interface to just solve without any normalization
read.SetData(sigVec, (int)nFlow);
}
else {
read.SetDataAndKeyNormalize(&(sigVec[0]), (int)nFlow, &(keyVec[0]), nKeyFlow-1);
}
// Execute the iterative solving-normalization routine
if (basecaller == "dp-treephaser") {
dpTreephaser.NormalizeAndSolve_GainNorm(read, nFlow);
}
else if (basecaller == "treephaser-solve") {
dpTreephaser.Solve(read, nFlow);
}
else if (basecaller == "treephaser-adaptive") {
dpTreephaser.NormalizeAndSolve_Adaptive(read, nFlow); // Adaptive normalization
}
else {
dpTreephaser.NormalizeAndSolve_SWnorm(read, nFlow); // sliding window adaptive normalization
}
seq_out[iRead].assign(read.sequence.begin(), read.sequence.end());
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++) {
predicted_out(iRead,iFlow) = (double) read.prediction[iFlow];
residual_out(iRead,iFlow) = (double) read.normalized_measurements[iFlow] - read.prediction[iFlow];
norm_multipl_out(iRead,iFlow) = (double) read.multiplicative_correction.at(iFlow);
norm_additive_out(iRead,iFlow) = (double) read.additive_correction.at(iFlow);
}
}
// Store results
ret = Rcpp::List::create(Rcpp::Named("seq") = seq_out,
Rcpp::Named("predicted") = predicted_out,
Rcpp::Named("residual") = residual_out,
Rcpp::Named("norm_additive") = norm_additive_out,
Rcpp::Named("norm_multipl") = norm_multipl_out);
}
} catch(std::exception& ex) {
forward_exception_to_r(ex);
} catch(...) {
::Rf_error("c++ exception (unknown reason)");
}
if(exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}
