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#ifndef __HIT_MANAGER_HPP__
#define __HIT_MANAGER_HPP__
#include "RapMapUtils.hpp"
#include "RapMapIndex.hpp"
#include "RapMapSAIndex.hpp"
//#include "eytzinger_array.h"
#include <tuple>
#include <vector>
#include <algorithm>
#include <map>
#include <unordered_map>
namespace rapmap {
namespace hit_manager {
using HitInfo = rapmap::utils::HitInfo;
using ProcessedHit = rapmap::utils::ProcessedHit;
using MateStatus = rapmap::utils::MateStatus;
using PositionListHelper = rapmap::utils::PositionListHelper;
using QuasiAlignment = rapmap::utils::QuasiAlignment;
using TxpQueryPos = rapmap::utils::TxpQueryPos;
using SATxpQueryPos = rapmap::utils::SATxpQueryPos;
template <typename T>
using SAIntervalHit = rapmap::utils::SAIntervalHit<T>;
using SAHitMap = std::map<int, rapmap::utils::ProcessedSAHit>;
using ProcessedSAHit = rapmap::utils::ProcessedSAHit;
class SAProcessedHitVec {
public:
std::vector<ProcessedSAHit> hits;
std::vector<uint32_t> txps;
};
/*
using SAProcessedHitVec = std::tuple<std::vector<ProcessedSAHit>, std::vector<uint32_t>>;
*/
// Return hits from processedHits where position constraints
// match maxDist
bool collectHitsSimple(std::vector<ProcessedHit>& processedHits,
uint32_t readLen,
uint32_t maxDist,
std::vector<QuasiAlignment>& hits,
MateStatus mateStatus);
// Return hits from processedHits where position constraints
// match maxDist
bool collectHitsSimpleSA(SAHitMap& processedHits,
uint32_t readLen,
uint32_t maxDist,
std::vector<QuasiAlignment>& hits,
MateStatus mateStatus);
// Return hits from processedHits where position constraints
// match maxDist
bool collectHitsSimpleSA2(std::vector<ProcessedSAHit>& processedHits,
uint32_t readLen,
uint32_t maxDist,
std::vector<QuasiAlignment>& hits,
MateStatus mateStatus);
// Intersects the hit h2 with outHits.
// This will modify outHits so that the tqvec field of the
// entries in outHits that are labeled by the transcripts in
// which h2 appears will have an iterator to the beginning of
// the position list for h2.
void intersectWithOutput(HitInfo& h2, RapMapIndex& rmi,
std::vector<ProcessedHit>& outHits);
template <typename RapMapIndexT>
void intersectSAIntervalWithOutput(SAIntervalHit<typename RapMapIndexT::IndexType>& h,
RapMapIndexT& rmi,
uint32_t intervalCounter,
SAHitMap& outHits);
template <typename RapMapIndexT>
void intersectSAIntervalWithOutput2(SAIntervalHit<typename RapMapIndexT::IndexType>& h,
RapMapIndexT& rmi,
SAProcessedHitVec& outStructs);
/*
void intersectSAIntervalWithOutput3(SAIntervalHit& h,
RapMapSAIndex& rmi,
SAProcessedHitVec& outHits);
*/
std::vector<ProcessedHit> intersectHits(
std::vector<HitInfo>& inHits,
RapMapIndex& rmi);
template <typename RapMapIndexT>
SAHitMap intersectSAHits(
std::vector<SAIntervalHit<typename RapMapIndexT::IndexType>>& inHits,
RapMapIndexT& rmi,
bool strictFilter=false);
template <typename RapMapIndexT>
std::vector<ProcessedSAHit> intersectSAHits2(
std::vector<SAIntervalHit<typename RapMapIndexT::IndexType>>& inHits,
RapMapIndexT& rmi);
}
}
#endif // __HIT_MANAGER_HPP__
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