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 struct __bcf_callaux_t {
18 int max_bases, capQ, min_baseQ;
23 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
26 if (theta <= 0.) theta = CALL_DEFTHETA;
27 bca = calloc(1, sizeof(bcf_callaux_t));
29 bca->min_baseQ = min_baseQ;
30 bca->e = errmod_init(1. - theta);
34 void bcf_call_destroy(bcf_callaux_t *bca)
37 errmod_destroy(bca->e);
38 free(bca->bases); free(bca);
41 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r)
44 memset(r, 0, sizeof(bcf_callret1_t));
45 ref4 = bam_nt16_nt4_table[ref_base];
46 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;
60 if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
61 baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality
62 if (q < bca->min_baseQ) continue;
63 mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
64 if (q > mapQ) q = mapQ;
67 b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
68 b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
69 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
70 // collect annotations
72 is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
73 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
74 min_dist = p->b->core.l_qseq - 1 - p->qpos;
75 if (min_dist > p->qpos) min_dist = p->qpos;
76 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
77 r->anno[1<<2|is_diff<<1|0] += baseQ;
78 r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
79 r->anno[2<<2|is_diff<<1|0] += mapQ;
80 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
81 r->anno[3<<2|is_diff<<1|0] += min_dist;
82 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
86 errmod_cal(bca->e, n, 5, bca->bases, r->p);
90 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
92 int ref4, i, j, qsum[4];
94 call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
95 if (ref4 > 4) ref4 = 4;
97 memset(qsum, 0, 4 * sizeof(int));
98 for (i = 0; i < n; ++i)
99 for (j = 0; j < 4; ++j)
100 qsum[j] += calls[i].qsum[j];
101 for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
102 // find the top 2 alleles
103 for (i = 1; i < 4; ++i) // insertion sort
104 for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
105 tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
106 // set the reference allele and alternative allele(s)
107 for (i = 0; i < 5; ++i) call->a[i] = -1;
110 for (i = 3, j = 1; i >= 0; --i) {
111 if ((qsum[i]&3) != ref4) {
112 if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
116 if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
117 call->unseen = j, call->a[j++] = qsum[i]&3;
122 call->PL = realloc(call->PL, 15 * n);
127 x = call->n_alleles * (call->n_alleles + 1) / 2;
128 // get the possible genotypes
129 for (i = z = 0; i < call->n_alleles; ++i)
130 for (j = i; j < call->n_alleles; ++j)
131 g[z++] = call->a[i] * 5 + call->a[j];
132 for (i = 0; i < n; ++i) {
133 uint8_t *PL = call->PL + x * i;
134 const bcf_callret1_t *r = calls + i;
136 for (j = 0; j < x; ++j)
137 if (min > r->p[g[j]]) min = r->p[g[j]];
139 for (j = 0; j < x; ++j) {
141 y = (int)(r->p[g[j]] - min + .499);
142 if (y > 255) y = 255;
146 call->shift = (int)(sum_min + .499);
148 // combine annotations
149 memset(call->anno, 0, 16 * sizeof(int));
150 for (i = call->depth = 0, tmp = 0; i < n; ++i) {
151 call->depth += calls[i].depth;
152 for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
157 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
161 b->tid = tid; b->pos = pos; b->qual = 0;
162 s.s = b->str; s.m = b->m_str; s.l = 0;
164 kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
165 for (i = 1; i < 5; ++i) {
166 if (bc->a[i] < 0) break;
167 if (i > 1) kputc(',', &s);
168 kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
174 for (i = 0; i < 16; ++i) {
175 if (i) kputc(',', &s);
176 kputw(bc->anno[i], &s);
180 kputs("PL", &s); kputc('\0', &s);
181 b->m_str = s.m; b->str = s.s; b->l_str = s.l;
183 memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);