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#ifndef ALIGNMENT_GROUP
#define ALIGNMENT_GROUP
extern "C" {
#include "io_lib/scram.h"
#include "io_lib/os.h"
#undef max
#undef min
}
// Cereal includes
#include "cereal/types/vector.hpp"
#include "cereal/archives/binary.hpp"
#include <vector>
#include "SalmonMath.hpp"
#include "ReadPair.hpp"
template <typename FragT>
class AlignmentGroup {
public:
AlignmentGroup() : read_(nullptr), isUniquelyMapped_(true) { alignments_.reserve(10); }
AlignmentGroup(AlignmentGroup& other) = delete;
AlignmentGroup(AlignmentGroup&& other) = default;
AlignmentGroup& operator=(AlignmentGroup& other) = delete;
AlignmentGroup& operator=(AlignmentGroup&& other) = delete;
void setRead(std::string* r) { read_ = r; }
std::string* read() { return read_; }
inline std::vector<FragT>& alignments() { return alignments_; }
void emplaceAlignment(FragT&& p) { alignments_.emplace_back(p); }
void addAlignment(FragT& p) { alignments_.push_back(p); }
void clearAlignments() {
alignments_.clear();
isUniquelyMapped_ = true;
}
inline bool& isUniquelyMapped() { return isUniquelyMapped_; }
inline size_t numAlignments() { return alignments_.size(); }
inline size_t size() { return numAlignments(); }
template <typename Archive>
void serialize(Archive& archive) {
archive(alignments_);
}
/**
* Sort the alignments by their transcript ids
*/
inline void sortHits() {
std::sort(alignments_.begin(), alignments_.end(),
[](const FragT& x, const FragT& y) -> bool {
return x->transcriptID() < y->transcriptID();
});
}
private:
std::vector<FragT> alignments_;
std::string* read_;
bool isUniquelyMapped_;
};
#endif // ALIGNMENT_GROUP
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