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
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
// Copyright 2010, 2013 Martin C. Frith
#include "gaplessXdrop.hh"
#include <stdexcept>
static void err(const char *s) { throw std::overflow_error(s); }
namespace cbrc {
int forwardGaplessXdropScore(const uchar *seq1,
const uchar *seq2,
const ScoreMatrixRow *scorer,
int maxScoreDrop) {
int score = 0;
int s = 0;
while (true) {
s += scorer[*seq1++][*seq2++]; // overflow risk
if (s < score - maxScoreDrop) break;
if (s > score) score = s;
}
if (score - s < 0)
err("score overflow in forward gapless extension");
return score;
}
int reverseGaplessXdropScore(const uchar *seq1,
const uchar *seq2,
const ScoreMatrixRow *scorer,
int maxScoreDrop) {
int score = 0;
int s = 0;
while (true) {
s += scorer[*--seq1][*--seq2]; // overflow risk
if (s < score - maxScoreDrop) break;
if (s > score) score = s;
}
if (score - s < 0)
err("score overflow in reverse gapless extension");
return score;
}
const uchar *forwardGaplessXdropEnd(const uchar *seq1,
const uchar *seq2,
const ScoreMatrixRow *scorer,
int score) {
int s = 0;
while (s < score) s += scorer[*seq1++][*seq2++];
return seq1;
}
const uchar *reverseGaplessXdropEnd(const uchar *seq1,
const uchar *seq2,
const ScoreMatrixRow *scorer,
int score) {
int s = 0;
while (s < score) s += scorer[*--seq1][*--seq2];
return seq1;
}
bool isOptimalGaplessXdrop(const uchar *seq1,
const uchar *seq1end,
const uchar *seq2,
const ScoreMatrixRow *scorer,
int maxScoreDrop) {
int score = 0;
int maxScore = 0;
while (seq1 < seq1end) {
score += scorer[*seq1++][*seq2++];
if (score > maxScore) maxScore = score;
else if (score <= 0 || // non-optimal prefix
seq1 == seq1end || // non-optimal suffix
score < maxScore - maxScoreDrop) { // excessive score drop
return false;
}
}
return true;
}
int gaplessXdropOverlap(const uchar *seq1,
const uchar *seq2,
const ScoreMatrixRow *scorer,
int maxScoreDrop,
size_t &reverseLength,
size_t &forwardLength) {
int minScore = 0;
int maxScore = 0;
int score = 0;
const uchar *r1 = seq1;
const uchar *r2 = seq2;
while (true) {
--r1; --r2;
int s = scorer[*r1][*r2];
if (s <= -INF) break;
score += s;
if (score > maxScore) maxScore = score;
else if (score < maxScore - maxScoreDrop) return -INF;
else if (score < minScore) minScore = score;
}
maxScore = score - minScore;
const uchar *f1 = seq1;
const uchar *f2 = seq2;
while (true) {
int s = scorer[*f1][*f2];
if (s <= -INF) break;
score += s;
if (score > maxScore) maxScore = score;
else if (score < maxScore - maxScoreDrop) return -INF;
++f1; ++f2;
}
reverseLength = seq1 - (r1 + 1);
forwardLength = f1 - seq1;
return score;
}
int gaplessAlignmentScore(const uchar *seq1,
const uchar *seq1end,
const uchar *seq2,
const ScoreMatrixRow *scorer) {
int score = 0;
while (seq1 < seq1end) score += scorer[*seq1++][*seq2++];
return score;
}
}
|
