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#ifndef __PAIR_ALIGNMENT_FORMATTER_HPP__
#define __PAIR_ALIGNMENT_FORMATTER_HPP__
#include "RapMapUtils.hpp"
template <typename IndexPtrT>
struct PairAlignmentFormatter {
PairAlignmentFormatter(IndexPtrT indexIn) : index(indexIn),
read1Temp(1000, 'A'),
qual1Temp(1000, '~'),
read2Temp(1000, 'A'),
qual2Temp(1000, '~'),
cigarStr1(buff1, 1000),
cigarStr2(buff2, 1000) {
}
// Data members
IndexPtrT index;
std::string read1Temp;
std::string qual1Temp;
std::string read2Temp;
std::string qual2Temp;
char buff1[1000];
char buff2[1000];
rapmap::utils::FixedWriter cigarStr1;
rapmap::utils::FixedWriter cigarStr2;
};
#endif //__PAIR_ALIGNMENT_FORMATTER_HPP__
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