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#ifndef FRAGMENT_LIST_HPP
#define FRAGMENT_LIST_HPP
extern "C" {
#include "container.h"
}
class FragmentList {
public:
FragmentList();
// Free all of the structures allocated for this fragment list
~FragmentList();
void freeFragList(Container* frags);
bool computeBestChain_(Container* frags, double& maxScore, uint32_t& bestPos);
void computeBestChain();
void addFragMatch(uint32_t refStart, uint32_t queryStart, uint32_t len);
void addFragMatch(uint32_t refStart, uint32_t refEnd,
uint32_t queryStart, uint32_t queryEnd);
void addFragMatchRC(uint32_t refStart, uint32_t queryStart, uint32_t len);
void addFragMatchRC(uint32_t refStart, uint32_t refEnd,
uint32_t queryStart, uint32_t queryEnd);
bool isForward();
Container* fragments;
Container* fragmentsRC;
size_t numFrag;
double bestHitScore;
uint32_t bestHitPos;
bool isForward_{true};
};
#endif // FRAGMENT_LIST_HPP
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