iVar

call_consensus.cpp
1 #include "htslib/vcf.h"
2
3 #include<iostream>
4 #include<fstream>
5
6 struct maj {
7 int *ind;
8 int n;
9 };
10
11 #define GET_MAX_INDICES(type_t, pu, no, m) { \
12 type_t v = 1; \
13 type_t *p = (type_t*) (pu); \
14 for (int k = 0; k < no; ++k){ \
15 if(p[k] > v){ \
16 v = p[k]; \
17 m.n = 0; \
18 m.ind[m.n] = k; \
19 } else if(p[k] == v) { \
20 m.n++; \
21 m.ind[m.n] = k; \
22 } \
23 } \
24 }
25
26 #define INDEL_SIZE 30
27
28 #define GAP 'N'
29
30 // From bcftools.h - https://github.com/samtools/bcftools/blob/b0376dff1ed70603c9490802f37883b9009215d2/bcftools.h#L48
31 static inline char gt2iupac(char a, char b)
32 {
33 static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} };
34 if ( a>='a' ) a -= 'a' - 'A';
35 if ( b>='a' ) b -= 'a' - 'A';
36 if ( a=='A' ) a = 0;
37 else if ( a=='C' ) a = 1;
38 else if ( a=='G' ) a = 2;
39 else if ( a=='T' ) a = 3;
40 else return 'N';
41 if ( b=='A' ) b = 0;
42 else if ( b=='C' ) b = 1;
43 else if ( b=='G' ) b = 2;
44 else if ( b=='T' ) b = 3;
45 else return 'N';
46 return iupac[(int)a][(int)b];
47 }
48
49 void get_consensus_indel(char **allele, maj m, char *&nuc){
50 int max_len = 0, l = 0;
51 uint8_t q = 0;
52 for (int k = 0; k <= m.n; ++k){
53 if(strlen(allele[m.ind[k]]) > max_len)
54 max_len = strlen(allele[m.ind[k]]);
55 }
56 char n;
57 for (int j = 0; j < max_len; ++j){ // Iterate over base positions
58 n = 0;
59 for (int k = 0; k <= m.n ; ++k){ // Iterate over major alleles
60 if(j < strlen(allele[m.ind[k]])){
61 if(n == 0){
62 n = allele[m.ind[k]][j];
63 } else {
64 n = gt2iupac(n, allele[m.ind[k]][j]);
65 }
66 }
67 }
68 if(n == 0)
69 nuc[l] = GAP;
70 else
71 nuc[l] = n;
72 l++;
73 if(l % INDEL_SIZE == 0){
74 nuc = (char*) realloc(nuc, INDEL_SIZE * ((l/INDEL_SIZE) + 1) * sizeof(char));
75 }
76 }
77 nuc[l] = 0;
78 }
79
80 int main_old(int argc, char* argv[]) {
81 std::cout << "Path " << argv[1] <<std::endl;
82 std::string bcf = std::string(argv[1]);
83 std::string region_;
84 std::string out_path = std::string(argv[2]);
85 if(argc > 3) {
86 region_ = std::string(argv[3]);
87 }
88 if(!bcf.empty()) {
89 //open BCF for reading
90 htsFile *in = bcf_open(bcf.c_str(), "r");
91 std::ofstream out(out_path);
92 out << ">" << out_path << "\n";
93 if(in == NULL) {
94 throw std::runtime_error("Unable to open BCF/VCF file.");
95 }
96 int ad_id;
97 //Get the header
98 bcf_hdr_t *header = bcf_hdr_read(in);
99 if(header == NULL) {
100 bcf_close(in);
101 throw std::runtime_error("Unable to open BCF header.");
102 }
103 ad_id = bcf_hdr_id2int(header, BCF_DT_ID, "AD");
104 std::cout << ad_id << " " << std::endl;
105 //Initialize iterator
106 bcf1_t *v = bcf_init();
107 int ctr = 0, prev_pos = 0, s, d;
108 maj m;
109 char *nuc =(char *) malloc(INDEL_SIZE * sizeof(char)), *r;
110 while(bcf_read(in, header, v) ==0){
111 // std::cout << "Position: " << v->pos << std::endl;
112 // std::cout << "Number of Alleles: " << v->n_allele << std::endl;
113 for (int i = prev_pos; i < v->pos - 1; ++i){
114 out << GAP;
115 }
116 bcf_unpack(v, BCF_UN_FMT);
117 bcf_unpack(v, BCF_UN_STR);
118 bcf_fmt_t *fmt = v->d.fmt;
119 for (int i = 0; i < v->n_fmt; ++i){
120 if(strcmp(header->id[BCF_DT_ID][fmt[i].id].key, "AD") == 0){
121 m.ind = (int *) malloc(fmt[i].n * sizeof(int));
122 m.n = -1;
123 switch(fmt[i].type){
124 case BCF_BT_INT8: GET_MAX_INDICES(int8_t, fmt[i].p, fmt[i].n, m); break;
125 case BCF_BT_INT16: GET_MAX_INDICES(int16_t, fmt[i].p, fmt[i].n, m); break;
126 case BCF_BT_INT32: GET_MAX_INDICES(int32_t, fmt[i].p, fmt[i].n, m); break;
127 case BCF_BT_FLOAT: GET_MAX_INDICES(float, fmt[i].p, fmt[i].n, m); break;
128 default: hts_log_error("Unexpected type %d", fmt[i].type); exit(1);
129 }
130 if(m.n == -1){
131 out << GAP;
132 } else {
133 if(bcf_get_variant_types(v) == VCF_REF){
134 out << v->d.allele[0];
135 } else if(bcf_get_variant_types(v) == VCF_SNP || bcf_get_variant_types(v) == VCF_MNP){
136 nuc =(char *) malloc(INDEL_SIZE * sizeof(char));
137 get_consensus_indel(v->d.allele, m, nuc);
138 out << nuc;
139 } else { // For INDEL insert difference.between reference and consensus allele
140 nuc =(char *) malloc(INDEL_SIZE * sizeof(char));
141 get_consensus_indel(v->d.allele, m, nuc);
142 s = strlen(v->d.allele[0]) - strlen(nuc); // > 0 Deletion. < 0 INSERTION
143 d = (s > 0) ? strlen(v->d.allele[0]) : strlen(nuc);
144 r = (s > 0) ? v->d.allele[0] : nuc;
145 s = (s < 0) ? -1 * s : s;
146 if(v->pos == 499)
147 std::cout << "Number: " << m.n << " Maj Allele: " << v->d.allele[m.ind[0]] << strlen(nuc) << " - Nuc Length" << nuc << " " << s << " " << d << std::endl;
148 for (int i = 0; i < s; ++i){
149 out << r[d - s];
150 }
151 free(m.ind);
152 free(nuc);
153 // std::cout << nuc << std::endl;
154 }
155 }
156 }
157 }
158 prev_pos = v->pos;
159 ctr++;
160 if(ctr % 1000 == 0){
161 std::cout << ctr << std::endl;
162 }
163 }
164 bcf_destroy(v);
165 bcf_hdr_destroy(header);
166 bcf_close(in);
167 out.close();
168 }
169 return 0;
170 }
allele
Definition: allele_functions.h:7
maj
Definition: call_consensus.cpp:6