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#ifndef _BLASR_SCORE_ANCHORS_HPP_
#define _BLASR_SCORE_ANCHORS_HPP_
#include <cmath>
#include <alignment/statistics/cdfs.hpp>
#include <alignment/statistics/pdfs.hpp>
#include <alignment/tuples/DNATuple.hpp>
#include <alignment/tuples/TupleCountTable.hpp>
#include <alignment/tuples/TupleMetrics.hpp>
template <typename TSequence, typename T_Tuple>
int GetTupleCount(TSequence &seq, DNALength startPos, TupleMetrics &tm,
TupleCountTable<TSequence, T_Tuple> &ct, int &count);
template <typename TSequence, typename T_Tuple>
int PMatch(TSequence &seq, DNALength startPos, DNALength length, TupleMetrics &tm,
TupleCountTable<TSequence, T_Tuple> &ct, float &pMatch);
template <typename TSequence, typename T_Tuple>
int POneOrMoreMatches(TSequence &seq, DNALength startPos, DNALength length, TupleMetrics &tm,
TupleCountTable<TSequence, T_Tuple> &ct, float &pValue);
template <typename TSequence, typename T_Tuple>
int SumRightShiftMarginalTupleCounts(TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
T_Tuple curTuple, int nextNuc, int &nextSeqCount);
template <typename TSequence, typename T_Tuple>
int ComputeTotalTupleCount(TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
TSequence &seq, int start = 0, int end = -1);
template <typename TSequence, typename T_Tuple>
int ComputeAverageTupleCount(TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
TSequence &seq);
inline int ComputeExpectedFirstWaitingTime(float lambda);
#include "ScoreAnchorsImpl.hpp"
#endif
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