6 #include "bcftools/bcf.h"
8 extern void ks_introsort_uint32_t(size_t n, uint32_t a[]);
10 #define CALL_ETA 0.03f
12 #define CALL_DEFTHETA 0.83f
16 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
19 if (theta <= 0.) theta = CALL_DEFTHETA;
20 bca = calloc(1, sizeof(bcf_callaux_t));
25 bca->min_baseQ = min_baseQ;
26 bca->e = errmod_init(1. - theta);
30 void bcf_call_destroy(bcf_callaux_t *bca)
33 errmod_destroy(bca->e);
34 free(bca->bases); free(bca);
37 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r)
40 memset(r, 0, sizeof(bcf_callret1_t));
41 ref4 = bam_nt16_nt4_table[ref_base];
42 if (_n == 0) return -1;
44 // enlarge the bases array if necessary
45 if (bca->max_bases < _n) {
47 kroundup32(bca->max_bases);
48 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
50 // fill the bases array
51 memset(r, 0, sizeof(bcf_callret1_t));
52 for (i = n = 0; i < _n; ++i) {
53 const bam_pileup1_t *p = pl + i;
54 int q, b, mapQ, baseQ, is_diff, min_dist;
56 if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
57 baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality
58 if (q < bca->min_baseQ) continue;
59 mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
60 if (q > mapQ) q = mapQ;
63 b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
64 b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
65 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
66 // collect annotations
68 is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
69 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
70 min_dist = p->b->core.l_qseq - 1 - p->qpos;
71 if (min_dist > p->qpos) min_dist = p->qpos;
72 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
73 r->anno[1<<2|is_diff<<1|0] += baseQ;
74 r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
75 r->anno[2<<2|is_diff<<1|0] += mapQ;
76 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
77 r->anno[3<<2|is_diff<<1|0] += min_dist;
78 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
82 errmod_cal(bca->e, n, 5, bca->bases, r->p);
86 int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r)
88 int i, n, n_ins, n_del;
89 memset(r, 0, sizeof(bcf_callret1_t));
90 if (_n == 0) return -1;
92 // enlarge the bases array if necessary
93 if (bca->max_bases < _n) {
95 kroundup32(bca->max_bases);
96 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
98 // fill the bases array
99 memset(r, 0, sizeof(bcf_callret1_t));
101 for (i = n = 0; i < _n; ++i) {
102 const bam_pileup1_t *p = pl + i;
103 int q, b, mapQ, indelQ, is_diff, min_dist;
104 if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
105 { // compute indel (base) quality
106 // this can be made more efficient, but realignment is the bottleneck anyway
107 int j, k, x, y, op, len = 0, max_left, max_rght, seqQ, indelreg;
108 bam1_core_t *c = &p->b->core;
109 uint32_t *cigar = bam1_cigar(p->b);
110 uint8_t *qual = bam1_qual(p->b);
111 for (k = y = 0, x = c->pos; k < c->n_cigar && y <= p->qpos; ++k) {
114 if (op == BAM_CMATCH) {
115 if (pos > x && pos < x + len) break;
117 } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += len;
118 else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += len;
120 if (k == c->n_cigar) continue; // this actually should not happen
121 max_left = max_rght = 0; indelreg = 0;
122 if (pos == x + len - 1 && k+2 < c->n_cigar && ((cigar[k+1]&0xf) == BAM_CINS || (cigar[k+1]&0xf) == BAM_CDEL)
123 && (cigar[k+2]&0xf) == BAM_CMATCH)
125 for (j = y; j < y + len; ++j)
126 if (max_left < qual[j]) max_left = qual[j];
127 if ((cigar[k+1]&0xf) == BAM_CINS) y += cigar[k+1]>>4;
128 else x += cigar[k+1]>>4;
129 op = cigar[k+2]&0xf; len = cigar[k+2]>>4;
130 for (j = y; j < y + len; ++j) {
131 if (max_rght < qual[j]) max_rght = qual[j];
132 if (qual[j] > BAM2BCF_INDELREG_THRES && indelreg == 0)
133 indelreg = j - y + 1;
136 for (j = y; j <= p->qpos; ++j)
137 if (max_left < qual[j]) max_left = qual[j];
138 for (j = p->qpos + 1; j < y + len; ++j)
139 if (max_rght < qual[j]) max_rght = qual[j];
142 indelQ = max_left < max_rght? max_left : max_rght;
143 // estimate the sequencing error rate
145 if (p->indel != 0) seqQ += bca->extQ * (abs(p->indel) - 1); // FIXME: better to model homopolymer
146 if (p->indel != 0) { // a different model for tandem repeats
147 uint8_t *seq = bam1_seq(p->b);
148 int tandemQ, qb = bam1_seqi(seq, p->qpos), l;
149 for (j = p->qpos + 1; j < c->l_qseq; ++j)
150 if (qb != bam1_seqi(seq, j)) break;
152 for (j = (int)p->qpos - 1; j >= 0; --j)
153 if (qb != bam1_seqi(seq, j)) break;
155 tandemQ = (int)((double)(abs(p->indel)) / l * bca->tandemQ + .499);
156 if (seqQ > tandemQ) seqQ = tandemQ;
158 // fprintf(stderr, "%s\t%d\t%d\t%d\t%d\t%d\t%d\n", bam1_qname(p->b), pos+1, p->indel, indelQ, seqQ, max_left, max_rght);
159 if (indelQ > seqQ) indelQ = seqQ;
162 if (q < bca->min_baseQ) continue;
163 mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
164 if (q > mapQ) q = mapQ;
168 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
169 // collect annotations
172 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
173 min_dist = p->b->core.l_qseq - 1 - p->qpos;
174 if (min_dist > p->qpos) min_dist = p->qpos;
175 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
176 r->anno[1<<2|is_diff<<1|0] += indelQ;
177 r->anno[1<<2|is_diff<<1|1] += indelQ * indelQ;
178 r->anno[2<<2|is_diff<<1|0] += mapQ;
179 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
180 r->anno[3<<2|is_diff<<1|0] += min_dist;
181 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
185 errmod_cal(bca->e, n, 2, bca->bases, r->p);
189 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
191 int ref4, i, j, qsum[4];
193 call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
194 if (ref4 > 4) ref4 = 4;
196 memset(qsum, 0, 4 * sizeof(int));
197 for (i = 0; i < n; ++i)
198 for (j = 0; j < 4; ++j)
199 qsum[j] += calls[i].qsum[j];
200 for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
201 // find the top 2 alleles
202 for (i = 1; i < 4; ++i) // insertion sort
203 for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
204 tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
205 // set the reference allele and alternative allele(s)
206 for (i = 0; i < 5; ++i) call->a[i] = -1;
209 for (i = 3, j = 1; i >= 0; --i) {
210 if ((qsum[i]&3) != ref4) {
211 if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
215 if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
216 call->unseen = j, call->a[j++] = qsum[i]&3;
221 call->PL = realloc(call->PL, 15 * n);
226 x = call->n_alleles * (call->n_alleles + 1) / 2;
227 // get the possible genotypes
228 for (i = z = 0; i < call->n_alleles; ++i)
229 for (j = i; j < call->n_alleles; ++j)
230 g[z++] = call->a[i] * 5 + call->a[j];
231 for (i = 0; i < n; ++i) {
232 uint8_t *PL = call->PL + x * i;
233 const bcf_callret1_t *r = calls + i;
235 for (j = 0; j < x; ++j)
236 if (min > r->p[g[j]]) min = r->p[g[j]];
238 for (j = 0; j < x; ++j) {
240 y = (int)(r->p[g[j]] - min + .499);
241 if (y > 255) y = 255;
245 call->shift = (int)(sum_min + .499);
247 // combine annotations
248 memset(call->anno, 0, 16 * sizeof(int));
249 for (i = call->depth = 0, tmp = 0; i < n; ++i) {
250 call->depth += calls[i].depth;
251 for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
256 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
258 extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
262 b->tid = tid; b->pos = pos; b->qual = 0;
263 s.s = b->str; s.m = b->m_str; s.l = 0;
265 kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
266 for (i = 1; i < 5; ++i) {
267 if (bc->a[i] < 0) break;
268 if (i > 1) kputc(',', &s);
269 kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
275 for (i = 0; i < 16; ++i) {
276 if (i) kputc(',', &s);
277 kputw(bc->anno[i], &s);
284 if (is_SP) kputs(":SP", &s);
287 b->m_str = s.m; b->str = s.s; b->l_str = s.l;
289 memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
291 uint16_t *dp = (uint16_t*)b->gi[1].data;
292 uint8_t *sp = is_SP? b->gi[2].data : 0;
293 for (i = 0; i < bc->n; ++i) {
294 bcf_callret1_t *p = bcr + i;
295 dp[i] = p->depth < 0xffff? p->depth : 0xffff;
297 if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
298 || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
302 double left, right, two;
304 kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
305 x = (int)(-4.343 * log(two) + .499);
306 if (x > 255) x = 255;