/usr/include/pbseq/alignment/algorithms/anchoring/ScoreAnchors.hpp is in libblasr-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | #ifndef _BLASR_SCORE_ANCHORS_HPP_
#define _BLASR_SCORE_ANCHORS_HPP_
#include <math.h>
#include "../../tuples/TupleCountTable.hpp"
#include "../../tuples/DNATuple.hpp"
#include "../../tuples/TupleMetrics.hpp"
#include "../../statistics/cdfs.hpp"
#include "../../statistics/pdfs.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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