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//
// RapMap - Rapid and accurate mapping of short reads to transcriptomes using
// quasi-mapping.
// Copyright (C) 2015, 2016 Rob Patro, Avi Srivastava, Hirak Sarkar
//
// This file is part of RapMap.
//
// RapMap is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// RapMap is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with RapMap. If not, see <http://www.gnu.org/licenses/>.
//
#ifndef __HIT_MANAGER_HPP__
#define __HIT_MANAGER_HPP__
#include "RapMapUtils.hpp"
#include "RapMapSAIndex.hpp"
#include "chobo/small_vector.hpp"
#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 ProcessedSAHit = rapmap::utils::ProcessedSAHit;
using SAHitMap = std::map<int, ProcessedSAHit>;
template <typename SAIntervalHitT>
using SAIntervalVector = std::vector<SAIntervalHitT>;
class SAProcessedHitVec {
public:
std::vector<ProcessedSAHit> hits;
std::vector<uint32_t> txps;
};
template <typename SAIntervalHitT>
class HitCollectorInfo {
public:
void clear() {
readLen = 0;
maxDist = 0;
fwdSAInts.clear();
rcSAInts.clear();
}
size_t readLen{0};
int32_t maxDist{0};
SAIntervalVector<SAIntervalHitT> fwdSAInts;
SAIntervalVector<SAIntervalHitT> rcSAInts;
};
/*
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,
int32_t maxDist,
std::vector<QuasiAlignment>& hits,
MateStatus mateStatus,
rapmap::utils::MappingConfig& mc);
// 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,
int32_t maxSlack,
SAHitMap& outHits);
template <typename RapMapIndexT>
void intersectSAIntervalWithOutput2(SAIntervalHit<typename RapMapIndexT::IndexType>& h,
RapMapIndexT& rmi,
SAProcessedHitVec& outStructs);
template <typename RapMapIndexT>
SAHitMap intersectSAHits(
SAIntervalVector<SAIntervalHit<typename RapMapIndexT::IndexType>>& inHits,
RapMapIndexT& rmi,
size_t readLen,
bool strictFilter=false);
template <typename RapMapIndexT>
void hitsToMappingsSimple(RapMapIndexT& rmi,
rapmap::utils::MappingConfig& mc,
rapmap::utils::MateStatus mateStatus,
HitCollectorInfo<SAIntervalHit<typename RapMapIndexT::IndexType>>& hcinfo,
std::vector<rapmap::utils::QuasiAlignment>& hits);
}
}
#endif // __HIT_MANAGER_HPP__
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