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#ifndef ALIGNMENT_MODEL
#define ALIGNMENT_MODEL
#include <mutex>
#include "AlignmentCommon.hpp"
#include "AtomicMatrix.hpp"
#include "oneapi/tbb/concurrent_vector.h"
class AlignmentModel
: public AlignmentCommon
{
public:
AlignmentModel(double alpha, uint32_t readBins = 4);
/**
* For unpaired reads, update the error model to account for errors
* we've observed in this read pair. primaryAln contains the first
* alignment in the alignment group.
*/
void update(const UnpairedRead& aln, const UnpairedRead& primaryAln,
Transcript& ref, double p, double mass);
/**
* Compute the log-likelihood of the observed unpaired alignment
* given the current error model. primaryAln contains the first
* alignment in the alignment group.
*/
double logLikelihood(const UnpairedRead&, const UnpairedRead& primaryAln, Transcript& ref);
// The primaryAln is ignored by the ReadPair overlaods (at least for now)
/**
* For paired-end reads, update the error model to account for
* errors we've observed in this read pair.
*/
void update(const ReadPair& aln, const ReadPair& primaryAln,
Transcript& ref, double p, double mass);
/**
* Compute the log-likelihood of the observed paire-end alignment given the
* current error model.
*/
double logLikelihood(const ReadPair& aln, const ReadPair& primaryAln, Transcript& ref);
void normalize();
private:
// std::stringstream& readStr, std::stringstream& matchStr,
// std::stringstream& refstr);
// 11 states --- the 9 listed in "AlignmentModelChar" plus START (9) i
// and END (10)
constexpr static uint32_t numAlignmentStates() { return 82; }
constexpr static uint32_t numStates = 9;
constexpr static uint32_t startStateIdx = 81;
struct AlnModelProb {
double fg{salmon::math::LOG_1};
double bg{salmon::math::LOG_1};
};
/**
* These functions, which work directly on bam_seq_t* types, drive the
* update() and logLikelihood() methods above.
*/
void update(bam_seq_t* read, bam_seq_t* primary, Transcript& ref, double p, double mass,
std::vector<AtomicMatrix<double>>& mismatchProfile);
AlnModelProb logLikelihood(bam_seq_t* read, bam_seq_t* primary, Transcript& ref,
std::vector<AtomicMatrix<double>>& mismatchProfile);
// NOTE: Do these need to be concurrent_vectors as before?
// Store the mismatch probability tables for the left and right reads
std::vector<AtomicMatrix<double>> transitionProbsLeft_;
std::vector<AtomicMatrix<double>> transitionProbsRight_;
bool isEnabled_;
// size_t maxLen_;
size_t readBins_;
// Maintain a mutex in case the error model wants to talk to the
// console / log.
std::mutex outputMutex_;
};
#endif // ERROR_MODEL
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