std::string
Individual::getChromosomeString (void) {
std::string result;
std::vector < bool > ch = getChromosome();
for (bool alel : ch) {
result.push_back ( alel?'1':'0' );
}
return result;
}
std::vector < Individual >
Individual::cruzaAcentuada (Individual& spouse) {
std::vector < Individual > result;
std::vector < bool > parent1 = getChromosome();
std::vector < bool > parent2 = spouse.getChromosome();
size_t size = parent1.size();
size_t genNumber = chromosome.size();
std::vector < bool > child1_ch, child2_ch, child1_marks(size, false), child2_marks(size, false);
bool cross = false;
std::vector <bool>::iterator mark_it = crossPoints.begin();
std::vector <bool>::iterator mark_spouse_it = spouse.crossPoints.begin();
for( size_t i = 0; i < size; i++, mark_it++, mark_spouse_it++ ) {
if (*mark_it || *mark_spouse_it) {
cross = !cross;
}
if(!cross) {
if(*mark_it) {
child2_marks.at(i) = true;
} if (*mark_spouse_it) {
child1_marks.at(i) = true;
}
child1_ch.push_back( parent1.at(i) );
child2_ch.push_back( parent2.at(i) );
} else {
if(*mark_it) {
child1_marks.at(i) = true;
} if (*mark_spouse_it) {
child2_marks.at(i) = true;
}
child1_ch.push_back( parent2.at(i) );
child2_ch.push_back( parent1.at(i) );
}
}
Individual child1 (child1_ch,genNumber);
Individual child2 (child2_ch,genNumber);
child1.crossPoints = child1_marks;
child2.crossPoints = child2_marks;
result.push_back( child1 );
result.push_back( child2 );
return result;
}
std::vector < Individual >
Individual::cruzaUnPunto (Individual& spouse, size_t p) {
std::vector < Individual > result;
std::vector < bool > parent1 = getChromosome();
std::vector < bool > parent2 = spouse.getChromosome();
std::vector < bool > child1, child2;
size_t size = parent1.size();
size_t genNumber = chromosome.size();
for( size_t i = 0; i < size; i++ ) {
if (i < p) {
child1.push_back( parent1.at(i) );
child2.push_back( parent2.at(i) );
} else {
child1.push_back( parent2.at(i) );
child2.push_back( parent1.at(i) );
}
}
result.push_back( Individual(child1,genNumber) );
result.push_back( Individual(child2,genNumber) );
return result;
}
std::vector < Individual >
Individual::cruzaDosPuntos (Individual& spouse, size_t x, size_t y) {
std::vector < Individual > result;
std::vector < bool > parent1 = getChromosome();
std::vector < bool > parent2 = spouse.getChromosome();
std::vector < bool > child1, child2;
size_t size = parent1.size();
size_t genNumber = chromosome.size();
size_t t = x;
x = x<y?x:y;
y = y<t?t:y;
for( size_t i = 0; i < size; i++ ) {
if (i < x || i >= y) {
child1.push_back( parent1.at(i) );
child2.push_back( parent2.at(i) );
} else {
child1.push_back( parent2.at(i) );
child2.push_back( parent1.at(i) );
}
}
result.push_back( Individual(child1,genNumber) );
result.push_back( Individual(child2,genNumber) );
return result;
}
void Chromosome<T>::copyChromosome(std::vector<T>& chromosome)
{
chromosome.clear();
for (unsigned int gen = 0; gen < size; ++gen)
chromosome.push_back(getChromosome()[gen]);
}
inline bool GenabelSnp::operator < (const GenabelSnp& snp) const {
int c1 = getChromosome();
int c2 = snp.getChromosome();
return c1 < c2 ? true : ( c1 > c2 ? false : getPosition() < snp.getPosition() );
}
void PileupElementBaseQual::analyze()
{
if(getRefPosition() != UNSET_POSITION && myIndex != -1)
{
char tempCStr[11];
std::string tempStr;
tempStr.append(getChromosome());
tempStr.append("\t");
sprintf(tempCStr, "%d", getRefPosition()+1 );
tempStr.append(tempCStr);
tempStr.append("\t.\t");
tempStr.append(getRefAllele());
tempStr.append("\t.\t.\t.\t.\t");
tempStr.append("N:BASE:MAPQ:BASEQ:STRAND:CYCLE:GL\t");
sprintf(tempCStr, "%d", myIndex+1 );
tempStr.append(tempCStr);
tempStr.append(":");
sprintf(tempCStr, "%c", myBases[0]);
tempStr.append(tempCStr);
for (int i=1; i<=myIndex; ++i)
{
sprintf(tempCStr, ",%c", myBases[i]);
tempStr.append(tempCStr);
}
tempStr.append(":");
sprintf(tempCStr, "%d", myMapQualities[0]);
tempStr.append(tempCStr);
for (int i=1; i<=myIndex; ++i)
{
sprintf(tempCStr, ",%d", myMapQualities[i]);
tempStr.append(tempCStr);
}
tempStr.append(":");
sprintf(tempCStr, "%d", myQualities[0]);
tempStr.append(tempCStr);
for (int i=1; i<=myIndex; ++i)
{
sprintf(tempCStr, ",%d", myQualities[i]);
tempStr.append(tempCStr);
}
tempStr.append(":");
sprintf(tempCStr, "%c", myStrands[0]);
tempStr.append(tempCStr);
for (int i=1; i<=myIndex; ++i)
{
sprintf(tempCStr, ",%c", myStrands[i]);
tempStr.append(tempCStr);
}
tempStr.append(":");
sprintf(tempCStr, "%d", myCycles[0]);
tempStr.append(tempCStr);
for (int i=1; i<=myIndex; ++i)
{
sprintf(tempCStr, ",%d", myCycles[i]);
tempStr.append(tempCStr);
}
tempStr.append(":");
computeGLScores(myIndex, myGLScores, myBases, myQualities);
sprintf(tempCStr, "%d", myGLScores[0]);
tempStr.append(tempCStr);
for (int i=1; i<=9; ++i)
{
sprintf(tempCStr, ",%d", myGLScores[i]);
tempStr.append(tempCStr);
}
tempStr.append("\n");
myVcfOutFile->ifwrite(tempStr.c_str(), tempStr.length());
}
//to ensure this does not print when reflushed
myIndex=-1;
}
// Add an entry to this pileup element.
void PileupElementBaseQual::addEntry(SamRecord& record)
{
// Call the base class:
PileupElement::addEntry(record);
if(myRefAllele.empty())
{
genomeIndex_t markerIndex = (*myRefSeq).getGenomePosition(getChromosome(), static_cast<uint32_t>(getRefPosition()+1));
myRefAllele = (*myRefSeq)[markerIndex];
}
// Increment the index
++myIndex;
// if the index has gone beyond the allocated space, double the size.
if(myIndex >= myAllocatedSize)
{
char* tempBuffer = (char*)realloc(myBases, myAllocatedSize * 2);
if(tempBuffer == NULL)
{
std::cerr << "Memory Allocation Failure\n";
// TODO
return;
}
myBases = tempBuffer;
int8_t* tempInt8Buffer = (int8_t*)realloc(myMapQualities, myAllocatedSize * 2 * sizeof(int8_t));
if(tempInt8Buffer == NULL)
{
std::cerr << "Memory Allocation Failure\n";
// TODO
return;
}
myMapQualities = tempInt8Buffer;
tempInt8Buffer = (int8_t*)realloc(myQualities, myAllocatedSize * 2 * sizeof(int8_t));
if(tempInt8Buffer == NULL)
{
std::cerr << "Memory Allocation Failure\n";
// TODO
return;
}
myQualities = tempInt8Buffer;
tempBuffer = (char*)realloc(myStrands, myAllocatedSize * 2);
if(tempBuffer == NULL)
{
std::cerr << "Memory Allocation Failure\n";
// TODO
return;
}
myStrands = tempBuffer;
tempInt8Buffer = (int8_t*)realloc(myCycles, myAllocatedSize * 2 * sizeof(int8_t));
if(tempInt8Buffer == NULL)
{
std::cerr << "Memory Allocation Failure\n";
// TODO
return;
}
myCycles = tempInt8Buffer;
int16_t* tempInt16Buffer = (int16_t*)realloc(myGLScores, myAllocatedSize * 2 * sizeof(int16_t));
if(tempInt8Buffer == NULL)
{
std::cerr << "Memory Allocation Failure\n";
// TODO
return;
}
myGLScores = tempInt16Buffer;
myAllocatedSize = myAllocatedSize * 2;
}
Cigar* cigar = record.getCigarInfo();
if(cigar == NULL)
{
throw std::runtime_error("Failed to retrieve cigar info from the record.");
}
int32_t readIndex =
cigar->getQueryIndex(getRefPosition(), record.get0BasedPosition());
// If the readPosition is N/A, this is a deletion.
if(readIndex != CigarRoller::INDEX_NA)
{
char base = record.getSequence(readIndex);
int8_t mapQual = record.getMapQuality();
//-33 to obtain the PHRED base quality
char qual = record.getQuality(readIndex) - 33;
if(qual == UNSET_QUAL)
{
qual = ' ';
}
char strand = (record.getFlag() & 0x0010) ? 'R' : 'F';
int cycle = strand == 'F' ? readIndex + 1 : record.getReadLength() - readIndex;
myBases[myIndex] = base;
myMapQualities[myIndex] = mapQual;
myQualities[myIndex] = qual;
myStrands[myIndex] = strand;
myCycles[myIndex] = cycle;
}
else if(myAddDelAsBase)
{
int8_t mapQual = record.getMapQuality();
char strand = (record.getFlag() & 0x0010) ? 'R' : 'F';
myBases[myIndex] = '-';
myMapQualities[myIndex] = mapQual;
myQualities[myIndex] = -1;
myStrands[myIndex] = strand;
myCycles[myIndex] = -1;
}
else
{
// Do not add a deletion.
// Did not add any entries, so decrement the index counter since the
// index was not used.
--myIndex;
}
}
