void HashErrorModel::addPrediction(Model model,int blendedWeight)
{
BaseData data;
if(ourUseFast)
{
return;
}
for(HashMatch::iterator it = mismatchTable.begin();
it != mismatchTable.end();
++it)
{
Covariates cov;
data.parseKey(it->first);
cov.setCovariates(data);
int j = 1;
double qemp = model[0]; //slope
for(std::vector<uint16_t>::const_iterator itv = cov.covariates.begin();
itv != cov.covariates.end(); ++itv)
{
qemp += model[j]*(double)(*itv);
j++;
}
//phred-score transformation
//conservative (otherwise +0.5)
//blended Model?
int phred = 0;
if(blendedWeight==9999)
{
uint32_t m = it->second.m;
uint32_t mm = it->second.mm;
qemp = (mm-blendedWeight)/(m+mm-blendedWeight);
}
else
{
if(blendedWeight>0)
{
uint32_t m = it->second.m;
uint32_t mm = it->second.mm;
//qemp = (mm+qemp*blendedWeight)/(m+mm+blendedWeight);
qemp = (mm+qemp*mm)/(2.0*(m+mm));
}
}
phred = trunc((-10.0*log10(1.0-(1.0/(1.0+exp(-qemp)))))+0.5);
it->second.qempLogReg = phred;
}
};
void HashErrorModel::setDataforPrediction(Matrix & X, Vector & succ, Vector & total,bool binarizeFlag)
{
int i = 0;
BaseData data;
if(ourUseFast)
{
return;
}
for(HashMatch::const_iterator it = mismatchTable.begin();
it != mismatchTable.end();
++it)
{
data.parseKey(it->first);
Covariates cov;
cov.setCovariates(data);
if(i == 0)
{
uint32_t rows = mismatchTable.size();
succ.Dimension(rows);
total.Dimension(rows);
X.Dimension(rows, cov.covariates.size() + 1);
X.Zero();
}
// The first column of the design matrix is constant one, for the slope
X[i][0] = 1.0;
int j = 0;
//binarize a couple of co-variates
for(std::vector<uint16_t>::const_iterator itv = cov.covariates.begin();
itv != cov.covariates.end();
++itv)
{
if(binarizeFlag)
{
//hardcoded pos is 2
if(j==1){
uint16_t pos = (uint16_t)*itv;
// hardcoded
pos += 7;
X[i][pos] = 1;
}
else
{
if(j>1)
X[i][j] = (uint16_t)*itv;
else
X[i][j+1] = (uint16_t)*itv;
}
j++;
}
else
{
X[i][j+1] = (uint16_t)*itv;
j++;
}
}
total[i] = it->second.mm + it->second.m;
succ[i] = it->second.m;
i++;
}
}
int HashErrorModel::writeTableQemp(std::string& filename,
const std::vector<std::string>& id2rg,
bool logReg)
{
FILE *pFile;
pFile = fopen(filename.c_str(), "w");
if(!pFile) return 0;
int maxId = id2rg.size() - 1;
BaseData data;
if(ourUseFast)
{
for(unsigned int i = 0; i < mismatchTableFast.size(); i++)
{
SMatchesFast& matchInfo = mismatchTableFast[i];
if((matchInfo.m == 0) && (matchInfo.mm == 0))
{
// No data, so continue to the next entry.
continue;
}
data.parseFastKey(i);
if(data.rgid <= maxId)
{
int16_t cycle = data.cycle + 1;
if(data.read)
{
// 2nd.
cycle = -cycle;
}
if(matchInfo.qempSimple == 255)
{
matchInfo.qempSimple =
getQempSimple(matchInfo.m, matchInfo.mm);
}
fprintf(pFile,"%s,%d,%d,%c%c,%d,%d,%d\n",
id2rg[data.rgid].c_str(), data.qual, cycle,
data.preBase, data.curBase,
matchInfo.m + matchInfo.mm, matchInfo.mm,
matchInfo.qempSimple);
}
}
fclose(pFile);
return(1);
}
for(HashMatch::iterator it = mismatchTable.begin();
it != mismatchTable.end();
++it)
{
data.parseKey(it->first);
if(data.rgid <= maxId)
{
int16_t cycle = data.cycle + 1;
if(data.read)
{
// 2nd.
cycle = -cycle;
}
if(it->second.qempSimple == 255)
{
it->second.qempSimple =
getQempSimple(it->second.m, it->second.mm);
}
uint8_t qemp = it->second.qempSimple;
if(logReg)
{
qemp = it->second.qempLogReg;
}
fprintf(pFile,"%s,%d,%d,%c%c,%d,%d,%d\n",
id2rg[data.rgid].c_str(), data.qual, cycle,
data.preBase, data.curBase,
it->second.m + it->second.mm, it->second.mm, qemp);
}
}
fclose(pFile);
return 1;
}
