std::vector<Location> Caller::callPoissonDist( double poissonLambda, int minQScore)
{
std::vector<Location> newCandidateLocations;
std::unordered_map<std::string, Location>::iterator iter;
std::string altBase;
for( iter = locationTable.begin(); iter != locationTable.end(); ++iter)
{
Location newLocation = iter->second;
// Clear the Sample list of the copy of the location
newLocation.clearSamples();
bool keepLocation = false;
std::vector<Sample> sampleList = ( iter->second).getSamples();
for( int i = 0; i < sampleList.size(); i++)
{
ReadcountEntry readcountEntry = sampleList[i].getReadcountEntry();
Allele mostFreqVariantAllele = readcountEntry.getMostFreqVariantAllele();
int mostFreqNonRefCount = mostFreqVariantAllele.getCount();
double lambda = readcountEntry.getReadDepth() * poissonLambda;
// call illuminaPoissonFilter
double pValue = Filter::illuminaPoissonFilter( mostFreqNonRefCount, lambda);
double qScore = -10 * std::log10( pValue);
// if at least one Sample passes through the filter, keep the location
if( qScore > minQScore)
{
//mostFreqVariantAllele.setPValue( pValue);
//mostFreqVariantAllele.setQScore( qScore);
// Add only the called Samples to the emptied list
newLocation.addSample( sampleList[i]);
keepLocation = true;
}
}
std::vector<Sample> newSamples = newLocation.getSamples();
double highestVAP = -1;
for( int i = 0; i < newSamples.size(); i++)
{
ReadcountEntry readcountEntry = newSamples[i].getReadcountEntry();
Allele variantAllele = readcountEntry.getMostFreqVariantAllele();
if( variantAllele.getPercentage() > highestVAP)
{
highestVAP = variantAllele.getPercentage();
altBase = variantAllele.getBase();
}
}
( iter->second).setMutatedBase( altBase);
if( keepLocation)
{
newCandidateLocations.push_back( newLocation);
}
}
return newCandidateLocations;
}
std::vector<Location> Caller::callAverageFilter( std::vector<Location> unfilteredCalls)
{
std::vector<Location> newCandidateLocations;
for( int i = 0; i < unfilteredCalls.size(); i++)
{
bool keepLocation = false;
// Make a copy of the Location for the new list of candidate locations
Location newLocation = unfilteredCalls[i];
// Clear the Sample list of the copy of the location
newLocation.clearSamples();
std::vector<Sample> sampleList = unfilteredCalls[i].getSamples();
int numSamples = sampleList.size();
for( int j = 0; j < numSamples; j++)
{
// Get the mean of the current location
double mean = unfilteredCalls[i].getMeanVAP();
double currentSamplePercentage = sampleList[j].getReadcountEntry().getMostFreqVariantAllele().getPercentage();
// If the current Sample's non reference percentage is 5 times or more greater than the new average, pass
if( currentSamplePercentage >= 3 * mean)
{
// If at least one Sample passes through the filter, keep the location
// Add only the called Samples to the emptied list
newLocation.addSample( sampleList[j]);
keepLocation = true;
}
}
if( keepLocation)
{
newCandidateLocations.push_back( newLocation);
}
}
return newCandidateLocations;
}
std::vector<Location> Caller::callStrandBiasFilter( std::vector<Location> unfilteredCalls, double strandBiasLeft, double strandBiasRight)
{
std::vector<Location> newCandidateLocations;
for( int i = 0; i < unfilteredCalls.size(); i++)
{
bool keepLocation = false;
// Make a copy of the Location for the new list of candidate locations
Location newLocation = unfilteredCalls[i];
// Clear the Sample list of the copy of the location
newLocation.clearSamples();
std::vector<Sample> sampleList = unfilteredCalls[i].getSamples();
int numSamples = sampleList.size();
for( int j = 0; j < numSamples; j++)
{
// Calculate the strand-bias
int numReadsForward = sampleList[j].getReadcountEntry().getMostFreqVariantAllele().getNumPlusStrand();
int numReadsReverse = sampleList[j].getReadcountEntry().getMostFreqVariantAllele().getNumMinusStrand();
double strandBias = ( double) numReadsForward / ( double) ( numReadsForward + numReadsReverse);
if( strandBias >= strandBiasLeft && strandBias <= strandBiasRight)
{
// If at least one Sample passes through the filter, keep the location
// Add only the called Samples to the emptied list
newLocation.addSample( sampleList[j]);
keepLocation = true;
}
}
if( keepLocation)
{
newCandidateLocations.push_back( newLocation);
}
}
return newCandidateLocations;
}
std::vector<Location> Caller::callAmpliconEndFilter( std::vector<Location> unfilteredCalls, double readEndFraction)
{
std::vector<Location> newCandidateLocations;
for( int i = 0; i < unfilteredCalls.size(); i++)
{
bool keepLocation = false;
// Make a copy of the Location for the new list of candidate locations
Location newLocation = unfilteredCalls[i];
// Clear the Sample list of the copy of the location
newLocation.clearSamples();
std::vector<Sample> sampleList = unfilteredCalls[i].getSamples();
int numSamples = sampleList.size();
for( int j = 0; j < numSamples; j++)
{
// Get average position on the reads as a fraction
double avgPosAsFraction = sampleList[j].getReadcountEntry().getMostFreqVariantAllele().getAvgPosAsFraction();
if( avgPosAsFraction >= readEndFraction)
{
// If at least one Sample passes through the filter, keep the location
// Add only the called Samples to the emptied list
newLocation.addSample( sampleList[j]);
keepLocation = true;
}
}
if( keepLocation)
{
newCandidateLocations.push_back( newLocation);
}
}
return newCandidateLocations;
}
std::vector<Location> Caller::callDepthFilter( std::vector<Location> unfilteredCalls, int minDepth)
{
std::vector<Location> newCandidateLocations;
for( int i = 0; i < unfilteredCalls.size(); i++)
{
bool keepLocation = false;
// Make a copy of the Location for the new list of candidate locations
Location newLocation = unfilteredCalls[i];
// Clear the Sample list of the copy of the location
newLocation.clearSamples();
std::vector<Sample> sampleList = unfilteredCalls[i].getSamples();
int numSamples = sampleList.size();
for( int j = 0; j < numSamples; j++)
{
// Get the read depth
int readDepth = sampleList[j].getReadcountEntry().getReadDepth();
if( readDepth >= minDepth)
{
// If at least one Sample passes through the filter, keep the location
// Add only the called Samples to the emptied list
newLocation.addSample( sampleList[j]);
keepLocation = true;
}
}
if( keepLocation)
{
newCandidateLocations.push_back( newLocation);
}
}
return newCandidateLocations;
}