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
|
// Author: David Alexander
#pragma once
#include <string>
#include <vector>
#include <ConsensusCore/Align/AlignConfig.hpp>
namespace {
// Utility functions common to implementations of aligners
inline int Max3(int a, int b, int c) { return std::max((a), std::max((b), (c))); }
inline int ArgMax3(int a, int b, int c)
{
if (a >= b && a >= c)
return 0;
else if (b >= c)
return 1;
else
return 2;
}
}
namespace ConsensusCore {
/// \brief A pairwise alignment
class PairwiseAlignment
{
private:
std::string target_;
std::string query_;
std::string transcript_;
public:
// target string, including gaps; usually the "reference"
std::string Target() const;
// query string, including gaps; usually the "read"
std::string Query() const;
// transcript as defined by Gusfield pg 215.
std::string Transcript() const;
public:
float Accuracy() const;
int Matches() const;
int Errors() const;
int Mismatches() const;
int Insertions() const;
int Deletions() const;
int Length() const;
public:
PairwiseAlignment(const std::string& target, const std::string& query);
static PairwiseAlignment* FromTranscript(const std::string& transcript,
const std::string& unalnTarget,
const std::string& unalnQuery);
};
PairwiseAlignment* Align(const std::string& target, const std::string& query, int* score,
AlignConfig config = AlignConfig::Default());
PairwiseAlignment* Align(const std::string& target, const std::string& query,
AlignConfig config = AlignConfig::Default());
// These calls return an array, same len as target, containing indices into the
// query string.
std::vector<int> TargetToQueryPositions(const std::string& transcript);
std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln);
}
|
