iVar

allele_functions.cpp
1 #include<string>
2 #include<vector>
3 #include<algorithm>
4 #include<iostream>
5
6 #include "allele_functions.h"
7
8 void print_allele_depths(std::vector<allele> ad){
9 std::cout << "AD Size: " << ad.size() << " " << std::endl;
10 for(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {
11 std::cout << "Nuc: " << it->nuc << std::endl;;
12 std::cout << "Depth: " << it->depth << std::endl;
13 std::cout << "Reverse: " << it->reverse <<std::endl;
14 std::cout << "Qual: " << (uint16_t) it->mean_qual << std::endl;
15 std::cout << "Beg: " << it->beg << std::endl;
16 std::cout << "End: " << it->end << std::endl;
17 }
18 }
19
20 int check_allele_exists(std::string n, std::vector<allele> ad){
21 for(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {
22 if(it->nuc.compare(n) == 0){
23 return it - ad.begin();
24 }
25 }
26 return -1;
27 }
28
29 int find_ref_in_allele(std::vector<allele> ad, char ref){
30 std::string ref_s(1, ref);
31 std::vector<allele>::iterator it = ad.begin();
32 while(it < ad.end()){
33 if(it->nuc.compare(ref_s) == 0)
34 return (it - ad.begin());
35 it++;
36 }
37 return -1;
38 }
39
40 std::vector<allele> update_allele_depth(char ref,std::string bases, std::string qualities, uint8_t min_qual){
41 std::vector<allele> ad;
42 std::string indel;
43 int i = 0, n =0, j = 0, q_ind = 0;
44 bool beg, end;
45 uint8_t q;
46 float num = 0, den = 0;
47 while (i < bases.length()){
48 beg = false;
49 end = false;
50 if(bases[i] == '^'){
51 i += 2; // Skip mapping quality as well (i+1) - 33
52 continue;
53 }
54 if(bases[i] == '$'){
55 i++;
56 continue;
57 }
58 q = qualities[q_ind] - 33;
59 std::string b;
60 allele tmp;
61 bool forward= true;
62 switch(bases[i]){
63 case '.':
64 b = ref;
65 end = (bases[i+1] == '$');
66 beg = (bases[i+1] == '^');
67 break;
68 case ',':
69 b = ref;
70 forward = false;
71 end = (bases[i+1] == '$');
72 beg = (bases[i+1] == '^');
73 break;
74 case '*':
75 b = bases[i];
76 break;
77 case '+': case '-':
78 j = i+1;
79 while(isdigit(bases[j])){
80 j++;
81 }
82 j = j - (i+1);
83 n = stoi(bases.substr(i+1, j));
84 indel = bases.substr(i+1+j, n);
85 transform(indel.begin(), indel.end(), indel.begin(),::toupper);
86 b = bases[i] + indel; // + for Insertion and - for Deletion
87 i += n + j;
88 if(indel[0]>=97 && indel[0] <= 122)
89 forward=false;
90 q = min_qual; // For insertions and deletion ust use minimum quality.
91 break;
92 default:
93 int asc_val = bases[i];
94 if(asc_val >= 65 && asc_val <= 90){
95 b = bases[i];
96 } else if(bases[i]>=97 && bases[i]<=122){
97 b = bases[i] - ('a' - 'A');
98 forward = false;
99 }
100 end = (bases[i+1] == '$');
101 beg = (bases[i+1] == '^');
102 }
103 int ind = check_allele_exists(b, ad);
104 if(q >= min_qual){
105 if (ind==-1){
106 tmp.nuc = b;
107 tmp.depth = 1;
108 tmp.tmp_mean_qual = q;
109 if(!forward)
110 tmp.reverse = 1;
111 else
112 tmp.reverse = 0;
113 if(beg)
114 tmp.beg = 1;
115 else
116 tmp.beg = 0;
117 if(end)
118 tmp.end = 1;
119 else
120 tmp.end = 0;
121 ad.push_back(tmp);
122 } else {
123 ad.at(ind).tmp_mean_qual = (ad.at(ind).tmp_mean_qual * ad.at(ind).depth + q)/(ad.at(ind).depth + 1);
124 ad.at(ind).depth += 1;
125 if(beg)
126 ad.at(ind).beg += 1;
127 if(end)
128 ad.at(ind).end += 1;
129 if(!forward)
130 ad.at(ind).reverse += 1;
131 }
132 }
133 i++;
134 if(b[0] !='+' && b[0]!='-')
135 q_ind++;
136 }
137 for(std::vector<allele>::iterator it = ad.begin(); it!=ad.end(); ++it){
138 it->mean_qual = (uint8_t) it->tmp_mean_qual;
139 }
140 if(ad.size() > 0)
141 std::sort(ad.begin(), ad.end());
142 return ad;
143 }
144
145 int get_index(char a){
146 switch(a){
147 case'Y':
148 a = 0;
149 break;
150 case'R':
151 a = 1;
152 break;
153 case'W':
154 a = 2;
155 break;
156 case'S':
157 a = 3;
158 break;
159 case'K':
160 a = 4;
161 break;
162 case'M':
163 a = 5;
164 break;
165 case'A':
166 a = 6;
167 break;
168 case'T':
169 a = 7;
170 break;
171 case'G':
172 a = 8;
173 break;
174 case'C':
175 a = 9;
176 break;
177 case'D':
178 a = 10;
179 break;
180 case'V':
181 a = 11;
182 break;
183 case'H':
184 a = 12;
185 break;
186 case'B':
187 a = 13;
188 break;
189 default:
190 a = -1;
191 }
192 return (int) a;
193 }
194
195 // Modified gt2iupac from bcftools.h. Expanded iupac matrix to include all ambigious nucleotides(added Y, R, W, S, K, M, A, T, G, C, D, V, H, B) - https://github.com/samtools/bcftools/blob/b0376dff1ed70603c9490802f37883b9009215d2/bcftools.h#L48
196 /*
197 Expanded IUPAC matrix:
198
199 Y N H B B H H Y B Y N N H B
200 N R D V D V R D R V D V N N
201 H D W N D H W W D H D N H N
202 B V N S B V V B S S N V N B
203 B D D B K N D K K B D N N B
204 H V H V N M M H V M N V H N
205 H R W V D M A W R M D V H N
206 Y D W B K H W T K Y D N H B
207 B R D S K V R K G S D V N B
208 Y V H S B M M Y S C N V H B
209 N D D N D N D D D N D N N N
210 N V N V N V V N V V N V N N
211 H N H N N H H H N H N N H N
212 B N N B B N N B B B N N N B
213
214 */
215 char gt2iupac(char a, char b){
216 if(a == '*' || b == '*')
217 return 'N';
218 static const char iupac[14][14] = {
219 {'Y', 'N', 'H', 'B', 'B', 'H', 'H', 'Y', 'B', 'Y', 'N', 'N', 'H', 'B'},
220 {'N', 'R', 'D', 'V', 'D', 'V', 'R', 'D', 'R', 'V', 'D', 'V', 'N', 'N'},
221 {'H', 'D', 'W', 'N', 'D', 'H', 'W', 'W', 'D', 'H', 'D', 'N', 'H', 'N'},
222 {'B', 'V', 'N', 'S', 'B', 'V', 'V', 'B', 'S', 'S', 'N', 'V', 'N', 'B'},
223 {'B', 'D', 'D', 'B', 'K', 'N', 'D', 'K', 'K', 'B', 'D', 'N', 'N', 'B'},
224 {'H', 'V', 'H', 'V', 'N', 'M', 'M', 'H', 'V', 'M', 'N', 'V', 'H', 'N'},
225 {'H', 'R', 'W', 'V', 'D', 'M', 'A', 'W', 'R', 'M', 'D', 'V', 'H', 'N'},
226 {'Y', 'D', 'W', 'B', 'K', 'H', 'W', 'T', 'K', 'Y', 'D', 'N', 'H', 'B'},
227 {'B', 'R', 'D', 'S', 'K', 'V', 'R', 'K', 'G', 'S', 'D', 'V', 'N', 'B'},
228 {'Y', 'V', 'H', 'S', 'B', 'M', 'M', 'Y', 'S', 'C', 'N', 'V', 'H', 'B'},
229 {'N', 'D', 'D', 'N', 'D', 'N', 'D', 'D', 'D', 'N', 'D', 'N', 'N', 'N'},
230 {'N', 'V', 'N', 'V', 'N', 'V', 'V', 'N', 'V', 'V', 'N', 'V', 'N', 'N'},
231 {'H', 'N', 'H', 'N', 'N', 'H', 'H', 'H', 'N', 'H', 'N', 'N', 'H', 'N'},
232 {'B', 'N', 'N', 'B', 'B', 'N', 'N', 'B', 'B', 'B', 'N', 'N', 'N', 'B'}
233 };
234 if ( a>='a' ) a -= 'a' - 'A';
235 if ( b>='a' ) b -= 'a' - 'A';
236 int _a, _b;
237 _a = get_index(a);
238 _b = get_index(b);
239 if(_a == -1 || _b == -1)
240 return 'N';
241 return iupac[_a][_b];
242 }
allele
Definition: allele_functions.h:7