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#include <cassert>
#include "Chromosome.h"
Chromosome::Chromosome(GenomeSequence* gs, unsigned int chromosomeIndex)
{
assert(gs);
assert(chromosomeIndex < (unsigned int)gs->getChromosomeCount());
this->gs = gs;
this->chromosomeIndex = chromosomeIndex;
this->offset = gs->getChromosomeStart((int)chromosomeIndex);
this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}
Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName)
{
assert(gs);
this->gs = gs;
this->chromosomeIndex = gs->getChromosome(chromosomeName);
assert(chromosomeIndex != INVALID_CHROMOSOME_INDEX);
this->offset = gs->getChromosomeStart((int)chromosomeIndex);
this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}
Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace)
{
std::string s(genomseSequenceFileName);
gs = new GenomeSequence;
assert(gs);
gs->setReferenceName(s);
assert(!gs->open(isColorSpace));
this->chromosomeIndex = chromosomeIndex;
this->offset = gs->getChromosomeStart((int)chromosomeIndex);
this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}
Chromosome::Chromosome(const std::string& genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace)
{
gs = new GenomeSequence;
assert(gs);
gs->setReferenceName(genomseSequenceFileName);
assert(!gs->open(isColorSpace));
this->chromosomeIndex = chromosomeIndex;
this->offset = gs->getChromosomeStart((int)chromosomeIndex);
this->chromosomeSize = gs->getChromosomeSize((int)chromosomeIndex);
}
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