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
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
|
#ifndef __BARCODE_MODEL_HPP__
#define __BARCODE_MODEL_HPP__
#include <iostream>
#include <string>
#include <vector>
#include <atomic>
#include <cmath>
#include "AlevinUtils.hpp"
#include "BarcodeGroup.hpp"
namespace alevin{
namespace model{
/*
Caluclates Probability argmax_A {P(b | A,d)}
*/
bool calculateAlnProbability(const std::string& s1,
const std::string& s2,
double& probability){
int32_t l1{static_cast<int32_t>(s1.size())}, l2 {static_cast<int32_t>(s2.size())};
// Shouldn't happen i.e. length diff are greater than 1
if ( std::abs(l1-l2) > 1 ){
probability = 0;
return false;
}
char edit{'M'};
uint32_t distance{0};
if(std::abs(l1-l2) == 1){
distance = 1;
}
for (int32_t i=0, j=0; i<l1 and j<l2; i++, j++){
if (s1[i] != s2[j]){
if (distance == 1){
edit = 'F';
break;
}
edit = 'S';
distance += 1;
if(l1-i==1 and l2-j==1){
break;
}
else{
bool flag = true;
if(s1[i+1] == s2[j+1]){
for(int32_t l=i+2, m=j+2; l<l1 and m<l2; l++,m++){
if (s1[l] != s2[m]){
flag = false;
break;
}
}
if (flag){
break;
}
}
}
if(s1[i+1] == s2[j]){
edit = 'D';
bool flag = true;
for(int32_t l=i+2, m=j+1; l<l1 and m<l2; l++,m++){
if (s1[l] != s2[m]){
flag = false;
break;
}
}
if (flag){
break;
}
}
if (s1[i] == s2[j+1]){
edit = 'I';
bool flag = true;
for(int32_t l=i+1, m=j+2; l<l1 and m<l2; l++,m++){
if (s1[l] != s2[m]){
flag = false;
break;
}
}
if (flag){
break;
}
}
edit = 'F';
break;
}
}
switch(edit){
case 'M': probability = 1.0;
break;
case 'S': probability = 0.6;//SNP
break;
case 'I': probability = 0.3;//Insertion
break;
case 'D': probability = 0.1;//deletion
break;
case 'F': probability = 0.0;
return false;
}
return true;
}
template <typename T>
std::vector<size_t> sort_indexes(const std::vector<T> &v,
const std::vector<std::string>& trueBarcodes) {
// initialize original index locations
std::vector<size_t> idx(v.size());
iota(idx.begin(), idx.end(), 0);
// sort indexes based on comparing values in v
sort(idx.begin(), idx.end(),
[&v, &trueBarcodes](size_t i1, size_t i2) {
if (v[i1] > v[i2])
return true;
else if (v[i1] < v[i2])
return false;
else
if (trueBarcodes[i1] > trueBarcodes[i2])
return true;
else
return false;
});
//if(v.size()>1 and v[idx[0]] == v[idx[1]]){
// size_t maxIdx = idx[0];
// size_t maxBase = 0;
// for (size_t qbase=1; qbase<v.size(); qbase++){
// size_t qIdx = idx[qbase];
// if (v[qIdx] < v[maxIdx]){
// break;
// }
// else if (v[qIdx] > v[maxIdx]) {
// std::cout << "ERROR in sorting the barcode probability" <<std::flush;
// exit(1);
// }
// if (trueBarcodes[qIdx].compare(trueBarcodes[maxIdx]) < 0){
// maxIdx = qIdx;
// maxBase = qbase;
// }
// }
// if (maxIdx != idx[0]){
// std::iter_swap(idx.begin(), idx.begin()+maxBase);
// }
//}
return idx;
}
void coinTossBarcodeModel(std::string barcode,
const std::vector<std::string>& trueBarcodes,
MapT& dumpPair){
if(trueBarcodes.size() == 1){
dumpPair.push_back(std::make_pair(trueBarcodes.front(), 1.0));
}
else{
std::vector<double> probabilityVec;
double alnProbability, probabilityNorm;
for(const std::string trueBarcode: trueBarcodes){
//save the sequence of the true barcodes for dumping
bool isOneEdit = calculateAlnProbability(trueBarcode,
barcode,
alnProbability);
if(!isOneEdit){
std::cerr << "Barcode model receveived wrong barcode mapping."
<< "should not happen, Please report the bug\n";
std::cerr << trueBarcode << "\n" << barcode <<std::endl;
std::exit(1);
}
probabilityVec.push_back(alnProbability);
}//end-for
//normalizer for the probability
probabilityNorm = std::accumulate(probabilityVec.begin(),
probabilityVec.end(),
0.0);
std::transform( probabilityVec.begin(), probabilityVec.end(),
probabilityVec.begin(),
[probabilityNorm](double n){ return n/probabilityNorm;} );
for (auto i: sort_indexes(probabilityVec, trueBarcodes)) {
dumpPair.push_back(std::make_pair(trueBarcodes[i], probabilityVec[i]));
}
//std::vector<double> cumProbVec(probabilityVec.size());
//std::partial_sum(probabilityVec.begin(), probabilityVec.end(),
// cumProbVec.begin());
//dumping the tuple (true barcode seq, cum. prob.).
//for(size_t i=0; i < trueBarcodes.size(); i++){
// dumpPair.push_back(std::make_pair(trueBarcodes[i], cumProbVec[i]));
//}
}//end-else
}
}
}
#endif
|
