/usr/include/pbseq/alignment/simulator/OutputSample.hpp is in libblasr-dev 0~20161219-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | #ifndef _SIMULATOR_OUTPUT_SAMPLE_HPP_
#define _SIMULATOR_OUTPUT_SAMPLE_HPP_
#include "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);
}
int 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));
int nNuc = nucleotides.size();
out.write((char*)&nNuc, sizeof(int));
int i;
for (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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