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#ifndef _SIMULATOR_OUTPUT_SAMPLE_HPP_
#define _SIMULATOR_OUTPUT_SAMPLE_HPP_
#include <alignment/simulator/QualitySample.hpp>
#include <pbdata/SMRTSequence.hpp>
class OutputSample
{
public:
enum Type
{
Match,
Insertion,
Deletion,
Substitution
};
std::vector<QualitySample> qualities;
std::vector<Nucleotide> nucleotides;
Type type;
void Resize(int size)
{
qualities.resize(size);
nucleotides.resize(size);
}
void CopyFromSeq(SMRTSequence &seq, int pos, int length = 1)
{
Resize(length);
int i;
for (i = 0; i < length; i++) {
qualities[i].CopyFromSequence(seq, pos + i);
nucleotides[i] = seq.seq[pos + i];
}
}
void Write(std::ofstream &out)
{
out.write((char *)&type, sizeof(type));
unsigned nNuc = nucleotides.size();
out.write((char *)&nNuc, sizeof(unsigned));
for (size_t i = 0; i < qualities.size(); i++) {
qualities[i].Write(out);
}
assert(nNuc == qualities.size());
out.write((char *)&nucleotides[0], sizeof(Nucleotide) * nucleotides.size());
}
void Read(std::ifstream &in)
{
in.read((char *)&type, sizeof(Type));
int nNuc;
in.read((char *)&nNuc, sizeof(int));
qualities.resize(nNuc);
int i;
for (i = 0; i < nNuc; i++) {
qualities[i].Read(in);
}
nucleotides.resize(nNuc);
in.read((char *)&nucleotides[0], sizeof(Nucleotide) * nNuc);
}
};
#endif
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