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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
/*
* Copyright (c) Medical Research Council 2000. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*
*/
#include <cassert>
#include <basecall.hpp>
//--------------
// Constructors
//--------------
void BaseCall::Init()
{
// Original data
Call = -1;
Position = -1;
Amplitude = -1;
Confidence = -1;
// New data
PeakCall = -1;
for( int n=0; n<4; n++ )
{
PeakPosition[n] = -1;
PeakAmplitude[n] = -1;
PeakWidth[n] = -1;
}
}
BaseCall::BaseCall()
{
Init();
}
BaseCall::BaseCall( int call, int pos, int conf )
{
Init();
Call = call;
Position = pos;
Confidence = conf;
}
BaseCall::BaseCall( int a, int c, int g, int t )
{
Init();
PeakAmplitude[0] = a;
PeakAmplitude[1] = c;
PeakAmplitude[2] = g;
PeakAmplitude[3] = t;
}
//--------------
// As Character
//--------------
char BaseCall::AsCharacter() const
{
const char Table[] = { '-', 'A', 'C', 'G', 'T' };
assert(Call>-2);
assert(Call<4);
return Table[Call+1];
}
//------------
// Peak Stuff
//------------
int BaseCall::PeakCount() const
{
int pc = 0;
if( PeakAmplitude[0] >= 0 ) pc++;
if( PeakAmplitude[1] >= 0 ) pc++;
if( PeakAmplitude[2] >= 0 ) pc++;
if( PeakAmplitude[3] >= 0 ) pc++;
return pc;
}
bool BaseCall::PeakPresent() const
{
if( (PeakAmplitude[0]>=0) || (PeakAmplitude[1]>=0) ||
(PeakAmplitude[2]>=0) || (PeakAmplitude[3]>=0) )
return true;
return false;
}
int BaseCall::Rank( std::size_t n, bool bIndex ) const
{
assert(n<4);
// Setup our call array
mutlib_pair_t c[4];
c[0].a = PeakAmplitude[0]; // Amplitude in a, index in b
c[0].b = 0;
c[1].a = PeakAmplitude[1];
c[1].b = 1;
c[2].a = PeakAmplitude[2];
c[2].b = 2;
c[3].a = PeakAmplitude[3];
c[3].b = 3;
// Do a quicksort, highest value last
if( c[0].a > c[1].a ) // 1st pair
Swap( c[0], c[1] );
if( c[2].a > c[3].a ) // 2nd pair
Swap( c[2], c[3] );
if( c[0].a > c[2].a ) // Tops
Swap( c[0], c[2] );
if( c[1].a > c[3].a ) // Bottoms
Swap( c[1], c[3] );
if( c[1].a > c[2].a ) // Middle
Swap( c[1], c[2] );
// Return nth highest value
return bIndex ? c[n].b : c[n].a;
}
int BaseCall::PeakOfRank( int n )
{
return Rank(n,false);
}
int BaseCall::PeakOfRankAsIndex( int n )
{
return Rank(n,true);
}
//------
// Swap
//------
void BaseCall::Swap( mutlib_pair_t& a, mutlib_pair_t& b ) const
{
mutlib_pair_t tmp = a;
a = b;
b = tmp;
}
|
