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#ifndef _BLASR_SAM_ALIGNMENT_SET_HPP_
#define _BLASR_SAM_ALIGNMENT_SET_HPP_
#include <map>
#include <string>
#include <vector>
#include "../FASTASequence.hpp"
#include "ReadGroup.hpp"
#include "ReferenceSequence.hpp"
#include "SAMAlignment.hpp"
#include "SAMHeader.hpp"
template<typename T_ReferenceSequence=SAMReferenceSequence, typename T_ReadGroup=SAMReadGroup, typename T_Alignment=SAMAlignment>
class AlignmentSet {
public:
SAMHeader header;
std::vector<T_ReferenceSequence> references;
std::vector<T_ReadGroup> readGroups;
std::vector<T_Alignment> alignments;
//
// Rearrange references such that they are placed in the same order
// as fastaReferences
//
void RearrangeReferences(std::vector<FASTASequence> & fastaReferences);
};
#include "AlignmentSetImpl.hpp"
#endif
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