std::string extendContigsWithCap3(const ReadSet & contigs,
ReadSet::ReadSetVector &contigReadSet, ReadSet & changedContigs,
ReadSet & finalContigs, ReadSet::ReadSetSizeType minimumCoverage) {
std::stringstream extendLog;
int poolsWithoutMinimumCoverage = 0;
// initialize per-thread Cap3 instances
Cap3 cap3[omp_get_max_threads()];
#pragma omp parallel for
for (long i = 0; i < (long) contigs.getSize(); i++) {
const Read &oldRead = contigs.getRead(i);
Read newRead = oldRead;
SequenceLengthType oldLen = oldRead.getLength(), newLen = 0;
ReadSet::ReadSetSizeType poolSize = contigReadSet[i].getSize();
double extTime = MPI_Wtime();
if (poolSize > minimumCoverage) {
LOG_VERBOSE_OPTIONAL(2, true, "Extending " << oldRead.getName() << " with " << poolSize << " pool of reads");
newRead = cap3[omp_get_thread_num()].extendContig(oldRead, contigReadSet[i]);
newLen = newRead.getLength();
} else {
poolsWithoutMinimumCoverage++;
}
extTime = MPI_Wtime() - extTime;
long deltaLen = (long)newLen - (long)oldLen;
if (deltaLen > 0) {
extendLog << std::endl << "Cap3 Extended " << oldRead.getName() << " "
<< deltaLen << " bases to " << newRead.getLength() << ": "
<< newRead.getName() << " with " << poolSize
<< " reads in the pool, in " << extTime << " sec";
//#pragma omp critical
changedContigs.append(newRead);
} else {
extendLog << std::endl << "Did not extend " << oldRead.getName() << " with " << poolSize << " reads in the pool, in " << extTime << " sec";
//#pragma omp critical
finalContigs.append(oldRead);
}
}
LOG_VERBOSE_OPTIONAL(2, true, "Extended " << contigs.getSize() - poolsWithoutMinimumCoverage << " contigs out of " << contigs.getSize());
return extendLog.str();
}
std::string extendContigsWithContigExtender(ReadSet & contigs,
ReadSet::ReadSetVector &contigReadSet, ReadSet & changedContigs,
ReadSet & finalContigs, SequenceLengthType minKmerSize,
double minimumCoverage, SequenceLengthType maxKmerSize,
SequenceLengthType maxExtend, SequenceLengthType kmerStep) {
std::stringstream extendLog;
//#pragma omp parallel for
for (ReadSet::ReadSetSizeType i = 0; i < contigs.getSize(); i++) {
const Read &oldRead = contigs.getRead(i);
Read newRead;
SequenceLengthType oldLen = oldRead.getLength(), newLen = 0;
ReadSet::ReadSetSizeType poolSize = contigReadSet[i].getSize();
SequenceLengthType myKmerSize = minKmerSize;
if (poolSize > minimumCoverage) {
LOG_VERBOSE_OPTIONAL(2, true, "kmer-Extending " << oldRead.getName() << " with " << poolSize << " pool of reads");
ReadSet myContig;
myContig.append(oldRead);
ReadSet newContig;
while (newLen <= oldLen && myKmerSize <= maxKmerSize) {
newContig = ContigExtender<KS>::extendContigs(myContig,
contigReadSet[i], maxExtend, myKmerSize, myKmerSize);
newLen = newContig.getRead(0).getLength();
myKmerSize += kmerStep;
}
newRead = newContig.getRead(0);
} else {
newRead = oldRead;
}
long deltaLen = (long) newLen - (long) oldLen;
if (deltaLen > 0) {
extendLog << std::endl << "Kmer Extended " << oldRead.getName() << " "
<< deltaLen << " bases to " << newRead.getLength() << ": "
<< newRead.getName() << " with " << poolSize
<< " reads in the pool K " << (myKmerSize - kmerStep);
//#pragma omp critical
changedContigs.append(newRead);
} else {
extendLog << std::endl << "Did not extend " << oldRead.getName() << " with " << poolSize << " reads in the pool";
//#pragma omp critical
finalContigs.append(oldRead);
}
}
return extendLog.str();
}
bool isContainment(){
return //length()==read.length();
length()>=read->getLength()*(1-percentMargin/100);
}
bool isLeftPart(){
return (isForward()&&begin!=0)||(!isForward()&&begin!=read->getLength()-1);
}
