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#ifndef ERROR_MODEL
#define ERROR_MODEL
#include <mutex>
#include <atomic>
#include "tbb/concurrent_vector.h"
#include "AtomicMatrix.hpp"
extern "C" {
#include "io_lib/scram.h"
#include "io_lib/os.h"
#undef max
#undef min
}
struct UnpairedRead;
struct ReadPair;
class Transcript;
class ErrorModel {
public:
ErrorModel(double alpha, uint32_t maxExpectedLen);
bool burnedIn();
void burnedIn(bool burnedIn);
/**
* For unpaired reads, update the error model to account
* for errors we've observed in this read pair.
*/
void update(const UnpairedRead&, Transcript& ref, double p, double mass);
/**
* Compute the log-likelihood of the observed unpaired alignment given the
* current error model.
*/
double logLikelihood(const UnpairedRead&, Transcript& ref);
/**
* For paired-end reads, update the error model to account
* for errors we've observed in this read pair.
*/
void update(const ReadPair&, 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&, Transcript& ref);
private:
/**
* These functions, which work directly on bam_seq_t* types, drive the
* update() and logLikelihood() methods above.
*/
void update(bam_seq_t* read, Transcript& ref, double p, double mass, std::vector<AtomicMatrix<double>>& mismatchProfile);
double logLikelihood(bam_seq_t* read, 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>> mismatchLeft_;
std::vector<AtomicMatrix<double>> mismatchRight_;
//tbb::concurrent_vector<AtomicMatrix<double>> mismatchLeft_;
//tbb::concurrent_vector<AtomicMatrix<double>> mismatchRight_;
bool isEnabled_;
size_t maxExpectedLen_;
size_t maxLen_;
std::atomic<bool> burnedIn_;
// 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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