/usr/include/blasr/algorithms/alignment/QualityValueScoreFunction.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
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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 47 48 49 50 51 52 53 54 55 56 | #ifndef _BLASR_QUALITY_VALUE_SCORE_FUNCTION_HPP_
#define _BLASR_QUALITY_VALUE_SCORE_FUNCTION_HPP_
#include "FASTASequence.hpp"
#include "FASTQSequence.hpp"
#include "NucConversion.hpp"
#include "ScoreMatrices.hpp"
#include "BaseScoreFunction.hpp"
template<typename T_RefSequence, typename T_QuerySequence>
class QualityValueScoreFunction: public BaseScoreFunction{
public:
int Deletion(T_RefSequence &seq, DNALength refPos,
T_QuerySequence &querySeq, DNALength queryPos);
int Deletion(T_RefSequence &seq, DNALength pos);
int Match(T_RefSequence &ref, DNALength refPos,
T_QuerySequence &query, DNALength queryPos);
int Insertion(T_RefSequence &ref, DNALength refPos,
T_QuerySequence &seq, DNALength pos);
int Insertion(T_QuerySequence &seq, DNALength pos);
};
//
// Define all specializations for a FASTA reference and
// FASTQSequence for the query, or FASTA sequence for query.
//
template<>
int QualityValueScoreFunction<FASTASequence, FASTQSequence>::Deletion(
FASTASequence &ref, DNALength pos);
template<>
int QualityValueScoreFunction<DNASequence, FASTQSequence>::Deletion(
DNASequence &ref, DNALength pos);
template<>
int QualityValueScoreFunction<DNASequence, FASTQSequence>::Deletion(
DNASequence &seq, DNALength refPos, FASTQSequence &querySeq,
DNALength queryPos);
template<>
int QualityValueScoreFunction<DNASequence, FASTQSequence>::Insertion(
FASTQSequence &query, DNALength pos);
template<>
int QualityValueScoreFunction<DNASequence, FASTQSequence>::Insertion(
DNASequence &ref, DNALength refPos, FASTQSequence &query,
DNALength pos);
template<>
int QualityValueScoreFunction<DNASequence, FASTQSequence>::Match(
DNASequence &ref, DNALength refPos, FASTQSequence &query,
DNALength queryPos);
#endif
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