7 #include "bcftools/bcf.h"
9 extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
11 #define CALL_ETA 0.03f
13 #define CALL_DEFTHETA 0.83f
17 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
20 if (theta <= 0.) theta = CALL_DEFTHETA;
21 bca = calloc(1, sizeof(bcf_callaux_t));
23 bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
24 bca->min_baseQ = min_baseQ;
25 bca->e = errmod_init(1. - theta);
26 bca->min_frac = 0.002;
31 void bcf_call_destroy(bcf_callaux_t *bca)
34 errmod_destroy(bca->e);
35 free(bca->bases); free(bca->inscns); free(bca);
37 /* ref_base is the 4-bit representation of the reference base. It is
38 * negative if we are looking at an indel. */
39 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
41 int i, n, ref4, is_indel, ori_depth = 0;
42 memset(r, 0, sizeof(bcf_callret1_t));
44 ref4 = bam_nt16_nt4_table[ref_base];
46 } else ref4 = 4, is_indel = 1;
47 if (_n == 0) return -1;
48 // enlarge the bases array if necessary
49 if (bca->max_bases < _n) {
51 kroundup32(bca->max_bases);
52 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
54 // fill the bases array
55 memset(r, 0, sizeof(bcf_callret1_t));
56 for (i = n = 0; i < _n; ++i) {
57 const bam_pileup1_t *p = pl + i;
58 int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
60 if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
62 baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
63 seqQ = is_indel? (p->aux>>8&0xff) : 99;
64 if (q < bca->min_baseQ) continue;
65 if (q > seqQ) q = seqQ;
66 mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
67 if (q > mapQ) q = mapQ;
71 b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
72 b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
73 is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
78 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
79 // collect annotations
81 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
82 min_dist = p->b->core.l_qseq - 1 - p->qpos;
83 if (min_dist > p->qpos) min_dist = p->qpos;
84 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
85 r->anno[1<<2|is_diff<<1|0] += baseQ;
86 r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
87 r->anno[2<<2|is_diff<<1|0] += mapQ;
88 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
89 r->anno[3<<2|is_diff<<1|0] += min_dist;
90 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
92 r->depth = n; r->ori_depth = ori_depth;
94 errmod_cal(bca->e, n, 5, bca->bases, r->p);
98 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
100 int ref4, i, j, qsum[4];
103 call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
104 if (ref4 > 4) ref4 = 4;
105 } else call->ori_ref = -1, ref4 = 0;
107 memset(qsum, 0, 4 * sizeof(int));
108 for (i = 0; i < n; ++i)
109 for (j = 0; j < 4; ++j)
110 qsum[j] += calls[i].qsum[j];
111 for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
112 // find the top 2 alleles
113 for (i = 1; i < 4; ++i) // insertion sort
114 for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
115 tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
116 // set the reference allele and alternative allele(s)
117 for (i = 0; i < 5; ++i) call->a[i] = -1;
120 for (i = 3, j = 1; i >= 0; --i) {
121 if ((qsum[i]&3) != ref4) {
122 if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
126 if (ref_base >= 0) { // for SNPs, find the "unseen" base
127 if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
128 call->unseen = j, call->a[j++] = qsum[i]&3;
132 if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
137 call->PL = realloc(call->PL, 15 * n);
142 x = call->n_alleles * (call->n_alleles + 1) / 2;
143 // get the possible genotypes
144 for (i = z = 0; i < call->n_alleles; ++i)
145 for (j = i; j < call->n_alleles; ++j)
146 g[z++] = call->a[i] * 5 + call->a[j];
147 for (i = 0; i < n; ++i) {
148 uint8_t *PL = call->PL + x * i;
149 const bcf_callret1_t *r = calls + i;
151 for (j = 0; j < x; ++j)
152 if (min > r->p[g[j]]) min = r->p[g[j]];
154 for (j = 0; j < x; ++j) {
156 y = (int)(r->p[g[j]] - min + .499);
157 if (y > 255) y = 255;
161 // if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
162 call->shift = (int)(sum_min + .499);
164 // combine annotations
165 memset(call->anno, 0, 16 * sizeof(int));
166 for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
167 call->depth += calls[i].depth;
168 call->ori_depth += calls[i].ori_depth;
169 for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
174 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
175 const bcf_callaux_t *bca, const char *ref)
177 extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
181 b->tid = tid; b->pos = pos; b->qual = 0;
182 s.s = b->str; s.m = b->m_str; s.l = 0;
184 if (bc->ori_ref < 0) { // an indel
187 for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
191 for (i = 1; i < 4; ++i) {
192 if (bc->a[i] < 0) break;
194 kputc(',', &s); kputc(ref[pos], &s);
196 if (bca->indel_types[bc->a[i]] < 0) { // deletion
197 for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
198 kputc(ref[pos+1+j], &s);
199 } else { // insertion; cannot be a reference unless a bug
200 char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
201 for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
202 kputc("ACGTN"[(int)inscns[j]], &s);
203 for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
208 kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
209 for (i = 1; i < 5; ++i) {
210 if (bc->a[i] < 0) break;
211 if (i > 1) kputc(',', &s);
212 kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
218 if (bc->ori_ref < 0) kputs("INDEL;", &s);
219 kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
220 for (i = 0; i < 16; ++i) {
221 if (i) kputc(',', &s);
222 kputw(bc->anno[i], &s);
229 if (is_SP) kputs(":SP", &s);
232 b->m_str = s.m; b->str = s.s; b->l_str = s.l;
234 memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
236 uint16_t *dp = (uint16_t*)b->gi[1].data;
237 uint8_t *sp = is_SP? b->gi[2].data : 0;
238 for (i = 0; i < bc->n; ++i) {
239 bcf_callret1_t *p = bcr + i;
240 dp[i] = p->depth < 0xffff? p->depth : 0xffff;
242 if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
243 || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
247 double left, right, two;
249 kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
250 x = (int)(-4.343 * log(two) + .499);
251 if (x > 255) x = 255;