/usr/include/blasr/algorithms/alignment/IDSScoreFunction.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 | #ifndef _BLASR_IDS_SCORE_FUNCTION_HPP_
#define _BLASR_IDS_SCORE_FUNCTION_HPP_
#include <string>
#include <cmath>
#include "ScoreMatrices.hpp"
#include "BaseScoreFunction.hpp"
#include "FASTASequence.hpp"
#include "FASTQSequence.hpp"
#include "utils/LogUtils.hpp"
float SumAsValidPhred(float v1, float v2, float v3);
template<typename T_RefSequence, typename T_QuerySequence>
class IDSScoreFunction : public BaseScoreFunction {
public:
int scoreMatrix[5][5];
IDSScoreFunction(int scoreMatrixP[5][5], int insertionP, int deletionP, int globalInsertionPriorP,
int globalDeletionPriorP) : BaseScoreFunction(insertionP, deletionP, globalInsertionPriorP, globalDeletionPriorP) {
InitializeScoreMatrix(scoreMatrixP);
}
IDSScoreFunction() {
substitutionPrior = 20;
globalDeletionPrior = 13;
}
void InitializeScoreMatrix(int scoreMatrixP[5][5]) {
int i, j;
for (i = 0; i < 5; i++ ){
for (j = 0; j < 5; j++ ){
scoreMatrix[i][j] = scoreMatrixP[i][j];
}
}
}
int Deletion(T_QuerySequence &seq, DNALength pos) {
std::cout << "IDS. For now, deletion must be specialized with FASTQ or FASTA Sequences. " << std::endl;
exit(1);
return 0;
}
int Deletion(T_RefSequence &refSeq, DNALength refPos, T_QuerySequence &querySeq, DNALength queryPos) {
std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences"<<std::endl;
exit(1);
}
int Match(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos) {
std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences" << std::endl;
return 0;
exit(1);
}
int Insertion(T_RefSequence &refSeq, DNALength refPos, T_QuerySequence &querySeq, DNALength queryPos) {
std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences"<<std::endl;
exit(1);
}
int Insertion(T_QuerySequence &seq, DNALength pos) {
std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences" << std::endl;
return 0;
exit(1);
}
float NormalizedMatch(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
float NormalizedInsertion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
float NormalizedDeletion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
};
/*
* Define all specializations for a FASTA reference and FASTQSequence for the query, or FASTA sequence for query.
*/
template<>
int IDSScoreFunction<DNASequence,FASTQSequence>::Deletion(DNASequence &ref,
DNALength refPos, FASTQSequence &query, DNALength queryPos);
template<>
int IDSScoreFunction<DNASequence, FASTQSequence>::Deletion(FASTQSequence &query,
DNALength queryPos);
template<>
int IDSScoreFunction<DNASequence, DNASequence>::Deletion(DNASequence &query,
DNALength pos);
template<>
int IDSScoreFunction<DNASequence, FASTQSequence>::Insertion(DNASequence &refSeq,
DNALength refPos, FASTQSequence &query, DNALength pos);
template<>
int IDSScoreFunction<DNASequence, FASTQSequence>::Insertion(FASTQSequence &query,
DNALength pos);
template<>
int IDSScoreFunction<DNASequence, FASTQSequence>::Match(DNASequence &ref,
DNALength refPos, FASTQSequence &query, DNALength queryPos);
template<>
float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedMatch(
DNASequence &ref, DNALength refPos, FASTQSequence &query, DNALength queryPos);
template<>
float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedInsertion(
DNASequence &ref, DNALength refPos, FASTQSequence &query, DNALength queryPos);
template<>
float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedDeletion(
DNASequence &ref, DNALength refPos, FASTQSequence &query, DNALength queryPos);
#endif // _BLASR_IDS_SCORE_FUNCTION_HPP_
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