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 phaseSolve(SEXP Rsignal, SEXP RflowCycle, SEXP RnucConc, SEXP Rcf, SEXP Rie, SEXP Rdr, SEXP RhpScale, SEXP RdroopType, SEXP RmaxAdv, SEXP RnIterations, SEXP RresidualScale, SEXP RresidualScaleMinFlow, SEXP RresidualScaleMaxFlow, SEXP RextraTaps, SEXP RdebugBaseCall)
{
SEXP ret = R_NilValue;
char *exceptionMesg = NULL;
try {
Rcpp::NumericMatrix signal(Rsignal);
string flowCycle = Rcpp::as<string>(RflowCycle);
Rcpp::NumericMatrix cc(RnucConc);
Rcpp::NumericVector cf(Rcf);
Rcpp::NumericVector ie(Rie);
Rcpp::NumericVector dr(Rdr);
Rcpp::NumericVector hpScale(RhpScale);
string drType = Rcpp::as<string>(RdroopType);
unsigned int maxAdv = (unsigned int) Rcpp::as<int>(RmaxAdv);
unsigned int nIterations = (unsigned int) Rcpp::as<int>(RnIterations);
unsigned int extraTaps = (unsigned int) Rcpp::as<int>(RextraTaps);
bool residualScale = Rcpp::as<bool>(RresidualScale);
int residualScaleMinFlow = Rcpp::as<int>(RresidualScaleMinFlow);
int residualScaleMaxFlow = Rcpp::as<int>(RresidualScaleMaxFlow);
bool debugBaseCall = Rcpp::as<bool>(RdebugBaseCall);
unsigned int nFlow = signal.cols();
unsigned int nRead = signal.rows();
DroopType droopType;
bool badDroopType = false;
if(drType == "ONLY_WHEN_INCORPORATING") {
droopType = ONLY_WHEN_INCORPORATING;
} else if(drType == "EVERY_FLOW") {
droopType = EVERY_FLOW;
} else {
badDroopType = true;
}
if(badDroopType) {
std::string exception = "bad droop type supplied\n";
exceptionMesg = strdup(exception.c_str());
} else if(cc.rows() != (int) N_NUCLEOTIDES) {
std::string exception = "concentration matrix should have 4 rows\n";
exceptionMesg = strdup(exception.c_str());
} else if(cc.cols() != (int) N_NUCLEOTIDES) {
std::string exception = "concentration matrix should have 4 columns\n";
exceptionMesg = strdup(exception.c_str());
} else {
// recast cf, ie, dr, hpScale
weight_vec_t cfMod(cf.size());
for(int i=0; i<cf.size(); i++)
cfMod[i] = cf(i);
weight_vec_t ieMod(ie.size());
for(int i=0; i<ie.size(); i++)
ieMod[i] = ie(i);
weight_vec_t drMod(dr.size());
for(int i=0; i<dr.size(); i++)
drMod[i] = dr(i);
weight_vec_t hpScaleMod(hpScale.size());
for(int i=0; i<hpScale.size(); i++)
hpScaleMod[i] = hpScale(i);
// recast nuc concentration
vector<weight_vec_t> ccMod(cc.rows());
for(int iRow=0; iRow < cc.rows(); iRow++) {
ccMod[iRow].resize(cc.cols());
for(unsigned int iCol=0; iCol < N_NUCLEOTIDES; iCol++)
ccMod[iRow][iCol] = cc(iRow,iCol);
}
// Other recasts
hpLen_t maxAdvMod = (hpLen_t) maxAdv;
// Prepare objects for holding and passing back results
Rcpp::NumericMatrix predicted_out(nRead,nFlow);
Rcpp::NumericMatrix residual_out(nRead,nFlow);
Rcpp::IntegerMatrix hpFlow_out(nRead,nFlow);
std::vector< std::string> seq_out(nRead);
Rcpp::NumericMatrix multiplier_out(nRead,1+nIterations);
// Iterate over all reads
weight_vec_t sigMod(nFlow);
string result;
for(unsigned int iRead=0; iRead < nRead; iRead++) {
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++)
sigMod[iFlow] = (weight_t) signal(iRead,iFlow);
PhaseSolve p;
p.SetResidualScale(residualScale);
if(residualScaleMinFlow >= 0)
p.SetResidualScaleMinFlow((unsigned int) residualScaleMinFlow);
if(residualScaleMaxFlow >= 0)
p.SetResidualScaleMaxFlow((unsigned int) residualScaleMaxFlow);
p.setExtraTaps(extraTaps);
p.setHpScale(hpScaleMod);
p.setPhaseParam(flowCycle,maxAdvMod,ccMod,cfMod,ieMod,drMod,droopType);
p.GreedyBaseCall(sigMod, nIterations, debugBaseCall);
p.getSeq(result);
seq_out[iRead] = result;
weight_vec_t & predicted = p.GetPredictedSignal();
weight_vec_t & residual = p.GetResidualSignal();
hpLen_vec_t & hpFlow = p.GetPredictedHpFlow();
for(unsigned int iFlow=0; iFlow < nFlow; iFlow++) {
predicted_out(iRead,iFlow) = (double) predicted[iFlow];
residual_out(iRead,iFlow) = (double) residual[iFlow];
hpFlow_out(iRead,iFlow) = (int) hpFlow[iFlow];
}
if(residualScale) {
weight_vec_t & multiplier = p.GetMultiplier();
// We re-order these so the last multiplier comes first. This is for convenience
// as it allows us grab the first col of the matrix as the last multiplier applied
// even if each read ended up taking different numbers of iterations.
unsigned int i1,i2;
for(i1=0,i2=multiplier.size()-1; i1 < multiplier.size(); i1++,i2--) {
multiplier_out(iRead,i1) = (double) multiplier[i2];
}
// If the read took fewer than all available iterations, pad with zero
for(; i1 <= nIterations; i1++) {
multiplier_out(iRead,i1) = 0;
}
}
}
// Store results
std::map<std::string,SEXP> map;
map["seq"] = Rcpp::wrap( seq_out );
map["predicted"] = Rcpp::wrap( predicted_out );
map["residual"] = Rcpp::wrap( residual_out );
map["hpFlow"] = Rcpp::wrap( hpFlow_out );
if(residualScale)
map["multiplier"] = Rcpp::wrap( multiplier_out );
ret = Rcpp::wrap( map );
}
} catch(std::exception& ex) {
forward_exception_to_r(ex);
} catch(...) {
::Rf_error("c++ exception (unknown reason)");
}
if(exceptionMesg != NULL)
Rf_error(exceptionMesg);
return ret;
}
