3 #include "bam_maqcns.h"
5 KSORT_INIT_GENERIC(uint32_t)
9 typedef struct __bmc_aux_t {
15 float esum[4], fsum[4];
20 char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
23 P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
24 P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
25 p_k = i/k / \sum_{i=1}^{N-1} 1/i
27 static void cal_het(bam_maqcns_t *aa)
30 double sum_harmo; // harmonic sum
32 double p1 = 0.0, p3 = 0.0; // just for testing
35 aa->lhet = (double*)calloc(256 * 256, sizeof(double));
37 for (k = 1; k <= aa->n_hap - 1; ++k)
39 for (n1 = 0; n1 < 256; ++n1) {
40 for (n2 = 0; n2 < 256; ++n2) {
41 long double sum = 0.0;
42 double lC = lgamma(n1+n2+1) - lgamma(n1+1) - lgamma(n2+1); // \binom{n1+n2}{n1}
43 for (k = 1; k <= aa->n_hap - 1; ++k) {
44 double pk = 1.0 / k / sum_harmo;
45 double log1 = log((double)k/aa->n_hap);
46 double log2 = log(1.0 - (double)k/aa->n_hap);
47 sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2));
49 aa->lhet[n1<<8|n2] = lC + logl(sum);
50 if (n1 == 17 && n2 == 3) p3 = lC + logl(expl(logl(0.5) * 20));
51 if (n1 == 19 && n2 == 1) p1 = lC + logl(expl(logl(0.5) * 20));
54 poly_rate = aa->het_rate * sum_harmo;
55 aa->q_r = -4.343 * log(2.0 * poly_rate / (1.0 - poly_rate));
58 /** initialize the helper structure */
59 static void cal_coef(bam_maqcns_t *aa)
62 long double sum_a[257], b[256], q_c[256], tmp[256], fk2[256];
65 lC = (double*)calloc(256 * 256, sizeof(double));
66 // aa->lhet will be allocated and initialized
67 free(aa->fk); free(aa->coef);
68 aa->fk = (double*)calloc(256, sizeof(double));
69 aa->coef = (double*)calloc(256*256*64, sizeof(double));
70 aa->fk[0] = fk2[0] = 1.0;
71 for (n = 1; n != 256; ++n) {
72 aa->fk[n] = pow(aa->theta, n) * (1.0 - aa->eta) + aa->eta;
73 fk2[n] = aa->fk[n>>1]; // this is an approximation, assuming reads equally likely come from both strands
75 for (n = 1; n != 256; ++n)
76 for (k = 1; k <= n; ++k)
77 lC[n<<8|k] = lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
78 for (q = 1; q != 64; ++q) {
79 double e = pow(10.0, -q/10.0);
81 double le1 = log(1.0-e);
82 for (n = 1; n != 256; ++n) {
83 double *coef = aa->coef + (q<<16|n<<8);
85 for (k = n; k >= 0; --k) { // a_k = \sum_{i=k}^n C^n_k \epsilon^k (1-\epsilon)^{n-k}
86 sum_a[k] = sum_a[k+1] + expl(lC[n<<8|k] + k*le + (n-k)*le1);
87 b[k] = sum_a[k+1] / sum_a[k];
88 if (b[k] > 0.99) b[k] = 0.99;
90 for (k = 0; k != n; ++k) // log(\bar\beta_{nk}(\bar\epsilon)^{f_k})
91 q_c[k] = -4.343 * fk2[k] * logl(b[k] / e);
92 for (k = 1; k != n; ++k) q_c[k] += q_c[k-1]; // \prod_{i=0}^k c_i
93 for (k = 0; k <= n; ++k) { // powl() in 64-bit mode seems broken on my Mac OS X 10.4.9
94 tmp[k] = -4.343 * logl(1.0 - expl(fk2[k] * logl(b[k])));
95 coef[k] = (k? q_c[k-1] : 0) + tmp[k]; // this is the final c_{nk}
102 bam_maqcns_t *bam_maqcns_init()
105 bm = (bam_maqcns_t*)calloc(1, sizeof(bam_maqcns_t));
106 bm->aux = (bmc_aux_t*)calloc(1, sizeof(bmc_aux_t));
107 bm->het_rate = 0.001;
114 void bam_maqcns_prepare(bam_maqcns_t *bm)
116 cal_coef(bm); cal_het(bm);
119 void bam_maqcns_destroy(bam_maqcns_t *bm)
122 free(bm->lhet); free(bm->fk); free(bm->coef); free(bm->aux->info);
123 free(bm->aux); free(bm);
126 glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm)
129 int i, j, k, w[8], c, n;
130 glf1_t *g = (glf1_t*)calloc(1, sizeof(glf1_t));
131 float p[16], min_p = 1e30;
134 g->ref_base = ref_base;
135 if (_n == 0) return g;
137 // construct aux array
138 if (bm->aux->max < _n) {
140 kroundup32(bm->aux->max);
141 bm->aux->info = (uint32_t*)realloc(bm->aux->info, 4 * bm->aux->max);
143 for (i = n = 0; i < _n; ++i) {
144 const bam_pileup1_t *p = pl + i;
146 if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
147 q = (uint32_t)bam1_qual(p->b)[p->qpos];
148 x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
149 if (p->b->core.qual < q) q = p->b->core.qual;
151 q = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
152 if (!p->is_del && q < 4) x |= 1 << 21 | q << 16;
153 bm->aux->info[n++] = x;
155 ks_introsort(uint32_t, n, bm->aux->info);
156 // generate esum and fsum
157 b = (glf_call_aux_t*)calloc(1, sizeof(glf_call_aux_t));
158 for (k = 0; k != 8; ++k) w[k] = 0;
160 for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
161 uint32_t info = bm->aux->info[j];
162 if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | (info&0xffffff);
165 b->esum[k&3] += bm->fk[w[k]] * (info>>24);
166 b->fsum[k&3] += bm->fk[w[k]];
167 if (w[k] < 0xff) ++w[k];
170 rms += (int)(info&0x7f) * (info&0x7f);
172 b->rms_mapQ = (uint8_t)(sqrt((double)rms / n) + .499);
174 for (j = c = 0; j != 4; ++j) c += b->c[j];
176 for (j = 0; j != 4; ++j) b->c[j] = (int)(254.0 * b->c[j] / c + 0.5);
177 for (j = c = 0; j != 4; ++j) c += b->c[j];
179 // generate likelihood
180 for (j = 0; j != 4; ++j) {
184 for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != 4; ++k) {
185 if (j == k) continue;
186 tmp1 += b->esum[k]; tmp2 += b->c[k]; tmp3 += b->fsum[k];
189 bar_e = (int)(tmp1 / tmp3 + 0.5);
190 if (bar_e < 4) bar_e = 4; // should not happen
191 if (bar_e > 63) bar_e = 63;
192 p[j<<2|j] = tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
193 } else p[j<<2|j] = 0.0; // all the bases are j
195 for (k = j + 1; k < 4; ++k) {
196 for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i != 4; ++i) {
197 if (i == j || i == k) continue;
198 tmp1 += b->esum[i]; tmp2 += b->c[i]; tmp3 += b->fsum[i];
201 bar_e = (int)(tmp1 / tmp3 + 0.5);
202 if (bar_e < 4) bar_e = 4;
203 if (bar_e > 63) bar_e = 63;
204 p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]] + tmp1 + bm->coef[bar_e<<16|c<<8|tmp2];
205 } else p[j<<2|k] = p[k<<2|j] = -4.343 * bm->lhet[b->c[j]<<8|b->c[k]]; // all the bases are either j or k
208 for (k = 0; k != 4; ++k)
209 if (p[j<<2|k] < 0.0) p[j<<2|k] = 0.0;
212 // convert necessary information to glf1_t
213 g->ref_base = ref_base; g->max_mapQ = b->rms_mapQ;
214 g->depth = n > 16777215? 16777215 : n;
215 for (j = 0; j != 4; ++j)
216 for (k = j; k < 4; ++k)
217 if (p[j<<2|k] < min_p) min_p = p[j<<2|k];
218 g->min_lk = min_p > 255.0? 255 : (int)(min_p + 0.5);
219 for (j = c = 0; j != 4; ++j)
220 for (k = j; k < 4; ++k)
221 g->lk[c++] = p[j<<2|k]-min_p > 255.0? 255 : (int)(p[j<<2|k]-min_p + 0.5);
227 uint32_t glf2cns(const glf1_t *g, int q_r)
229 int i, j, k, tmp[16], min = 10000, min2 = 10000, min3 = 10000, min_g = -1, min_g2 = -1;
231 for (i = k = 0; i < 4; ++i)
232 for (j = i; j < 4; ++j) {
234 tmp[i<<2|j] = g->lk[k++] + (i == j? 0 : q_r);
236 for (i = 0; i < 16; ++i) {
237 if (tmp[i] < 0) continue;
239 min3 = min2; min2 = min; min = tmp[i]; min_g2 = min_g; min_g = i;
240 } else if (tmp[i] < min2) {
241 min3 = min2; min2 = tmp[i]; min_g2 = i;
242 } else if (tmp[i] < min3) min3 = tmp[i];
244 x = min_g >= 0? (1U<<(min_g>>2&3) | 1U<<(min_g&3)) << 28 : 0xf << 28;
245 x |= min_g2 >= 0? (1U<<(min_g2>>2&3) | 1U<<(min_g2&3)) << 24 : 0xf << 24;
246 x |= (uint32_t)g->max_mapQ << 16;
247 x |= min2 < 10000? (min2 - min < 256? min2 - min : 255) << 8 : 0xff << 8;
248 x |= min2 < 10000 && min3 < 10000? (min3 - min2 < 256? min3 - min2 : 255) : 0xff;
252 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm)
257 g = bam_maqcns_glfgen(n, pl, 0xf, bm);
258 x = glf2cns(g, (int)(bm->q_r + 0.5));
260 } else x = 0xfU<<28 | 0xfU<<24;
264 /************** *****************/
266 bam_maqindel_opt_t *bam_maqindel_opt_init()
268 bam_maqindel_opt_t *mi = (bam_maqindel_opt_t*)calloc(1, sizeof(bam_maqindel_opt_t));
270 mi->r_indel = 0.00015;
278 void bam_maqindel_ret_destroy(bam_maqindel_ret_t *mir)
280 if (mir == 0) return;
281 free(mir->s[0]); free(mir->s[1]); free(mir);
284 #define MINUS_CONST 0x10000000
286 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
287 int _n_types, int *_types)
289 int i, j, n_types, *types, left, right;
290 bam_maqindel_ret_t *ret = 0;
291 // if there is no proposed indel, check if there is an indel from the alignment
293 for (i = 0; i < n; ++i) {
294 const bam_pileup1_t *p = pl + i;
295 if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0) break;
297 if (i == n) return 0; // no indel
299 { // calculate how many types of indels are available (set n_types and types)
302 aux = (uint32_t*)calloc(n + _n_types + 1, 4);
304 aux[m++] = MINUS_CONST; // zero indel is always a type
305 for (i = 0; i < n; ++i) {
306 const bam_pileup1_t *p = pl + i;
307 if (!(p->b->core.flag&BAM_FUNMAP) && p->indel != 0)
308 aux[m++] = MINUS_CONST + p->indel;
310 if (_n_types) // then also add this to aux[]
311 for (i = 0; i < _n_types; ++i)
312 if (_types[i]) aux[m++] = MINUS_CONST + _types[i];
313 ks_introsort(uint32_t, m, aux);
314 // squeeze out identical types
315 for (i = 1, n_types = 1; i < m; ++i)
316 if (aux[i] != aux[i-1]) ++n_types;
317 types = (int*)calloc(n_types, sizeof(int));
319 types[j++] = aux[0] - MINUS_CONST;
320 for (i = 1; i < m; ++i) {
321 if (aux[i] != aux[i-1])
322 types[j++] = aux[i] - MINUS_CONST;
326 { // calculate left and right boundary
328 left = 0x7fffffff; right = 0;
329 for (i = 0; i < n; ++i) {
330 const bam_pileup1_t *p = pl + i;
331 if (!(p->b->core.flag&BAM_FUNMAP)) {
332 bam_segreg(pos, &p->b->core, bam1_cigar(p->b), &seg);
333 if (seg.tbeg < left) left = seg.tbeg;
334 if (seg.tend > right) right = seg.tend;
337 if (pos - left > MAX_WINDOW) left = pos - MAX_WINDOW;
338 if (right - pos> MAX_WINDOW) right = pos + MAX_WINDOW;
341 char *ref2, *inscns = 0;
342 int k, l, *score, *pscore, max_ins = types[n_types-1];
343 ref2 = (char*)calloc(right - left + types[n_types-1] + 2, 1);
344 if (max_ins > 0) { // get the consensus of inserted sequences
345 int *inscns_aux = (int*)calloc(4 * n_types * max_ins, sizeof(int));
347 for (i = 0; i < n_types; ++i) {
348 if (types[i] <= 0) continue; // not insertion
349 for (j = 0; j < n; ++j) {
350 const bam_pileup1_t *p = pl + j;
351 if (!(p->b->core.flag&BAM_FUNMAP) && p->indel == types[i]) {
352 for (k = 1; k <= p->indel; ++k) {
353 int c = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos + k)];
354 if (c < 4) ++inscns_aux[i*max_ins*4 + (k-1)*4 + c];
359 // construct the consensus of inserted sequence
360 inscns = (char*)calloc(n_types * max_ins, sizeof(char));
361 for (i = 0; i < n_types; ++i) {
362 for (j = 0; j < types[i]; ++j) {
363 int max = 0, max_k = -1, *ia = inscns_aux + i*max_ins*4 + j*4;
364 for (k = 0; k < 4; ++k) {
370 inscns[i*max_ins + j] = max? 1<<max_k : 15;
376 score = (int*)calloc(n_types * n, sizeof(int));
377 pscore = (int*)calloc(n_types * n, sizeof(int));
378 for (i = 0; i < n_types; ++i) {
380 for (k = 0, j = left; j <= pos; ++j)
381 ref2[k++] = bam_nt16_table[(int)ref[j]];
382 if (types[i] <= 0) j += -types[i];
383 else for (l = 0; l < types[i]; ++l)
384 ref2[k++] = inscns[i*max_ins + l];
385 for (; j < right && ref[j]; ++j)
386 ref2[k++] = bam_nt16_table[(int)ref[j]];
387 // calculate score for each read
388 for (j = 0; j < n; ++j) {
389 const bam_pileup1_t *p = pl + j;
391 bam1_core_t *c = &p->b->core;
394 if (c->flag&BAM_FUNMAP) continue;
395 cigar = bam1_cigar(p->b);
396 bam_segreg(pos, c, cigar, &seg);
397 for (ps = s = 0, l = seg.qbeg; c->pos + l < right && l < seg.qend; ++l) {
398 int cq = bam1_seqi(bam1_seq(p->b), l), ct;
399 ct = c->pos + l >= left? ref2[c->pos + l - left] : 15; // "<" will happen if reads are too long
400 if (cq < 15 && ct < 15) {
401 s += cq == ct? 1 : -mi->mm_penalty;
402 if (cq != ct) ps += bam1_qual(p->b)[l];
405 score[i*n + j] = s; pscore[i*n + j] = ps;
406 if (types[i] != 0) { // then try the other way to calculate the score
407 for (ps = s = 0, l = seg.qbeg; c->pos + l + types[i] < right && l < seg.qend; ++l) {
408 int cq = bam1_seqi(bam1_seq(p->b), l), ct;
409 ct = c->pos + l + types[i] >= left? ref2[c->pos + l + types[i] - left] : 15;
410 if (cq < 15 && ct < 15) {
411 s += cq == ct? 1 : -mi->mm_penalty;
412 if (cq != ct) ps += bam1_qual(p->b)[l];
416 if (score[i*n+j] < s) score[i*n+j] = s; // choose the higher of the two scores
417 if (pscore[i*n+j] > ps) pscore[i*n+j] = ps;
418 if (types[i] != 0) score[i*n+j] -= mi->indel_err;
419 //printf("%d, %d, %d, %d\n", i, types[i], j, score[i*n+j]);
422 { // get final result
423 int *sum, max1, max2, max1_i, max2_i;
424 // pick up the best two score
425 sum = (int*)calloc(n_types, sizeof(int));
426 for (i = 0; i < n_types; ++i)
427 for (j = 0; j < n; ++j)
428 sum[i] += -pscore[i*n+j];
429 max1 = max2 = -0x7fffffff; max1_i = max2_i = -1;
430 for (i = 0; i < n_types; ++i) {
432 max2 = max1; max2_i = max1_i; max1 = sum[i]; max1_i = i;
433 } else if (sum[i] > max2) {
434 max2 = sum[i]; max2_i = i;
439 ret = (bam_maqindel_ret_t*)calloc(1, sizeof(bam_maqindel_ret_t));
440 ret->indel1 = types[max1_i]; ret->indel2 = types[max2_i];
441 ret->s[0] = (char*)calloc(abs(ret->indel1) + 2, 1);
442 ret->s[1] = (char*)calloc(abs(ret->indel2) + 2, 1);
443 // write indel sequence
444 if (ret->indel1 > 0) {
446 for (k = 0; k < ret->indel1; ++k)
447 ret->s[0][k+1] = bam_nt16_rev_table[(int)inscns[max1_i*max_ins + k]];
448 } else if (ret->indel1 < 0) {
450 for (k = 0; k < -ret->indel1 && ref[pos + k + 1]; ++k)
451 ret->s[0][k+1] = ref[pos + k + 1];
452 } else ret->s[0][0] = '*';
453 if (ret->indel2 > 0) {
455 for (k = 0; k < ret->indel2; ++k)
456 ret->s[1][k+1] = bam_nt16_rev_table[(int)inscns[max2_i*max_ins + k]];
457 } else if (ret->indel2 < 0) {
459 for (k = 0; k < -ret->indel2 && ref[pos + k + 1]; ++k)
460 ret->s[1][k+1] = ref[pos + k + 1];
461 } else ret->s[1][0] = '*';
463 for (i = 0; i < n; ++i) {
464 const bam_pileup1_t *p = pl + i;
465 if (p->indel == ret->indel1) ++ret->cnt1;
466 else if (p->indel == ret->indel2) ++ret->cnt2;
467 else ++ret->cnt_anti;
470 ret->gl[0] = ret->gl[1] = 0;
471 for (j = 0; j < n; ++j) {
472 int s1 = pscore[max1_i*n + j], s2 = pscore[max2_i*n + j];
473 //printf("%d, %d\n", s1, s2);
474 if (s1 > s2) ret->gl[0] += s1 - s2 < mi->q_indel? s1 - s2 : mi->q_indel;
475 else ret->gl[1] += s2 - s1 < mi->q_indel? s2 - s1 : mi->q_indel;
478 free(score); free(pscore); free(ref2); free(inscns);
481 int q[3], qr_indel = (int)(-4.343 * log(mi->r_indel) + 0.5);
482 int min1, min2, min1_i;
483 q[0] = ret->gl[0] + (ret->s[0][0] != '*'? 0 : 0) * qr_indel;
484 q[1] = ret->gl[1] + (ret->s[1][0] != '*'? 0 : 0) * qr_indel;
485 q[2] = n * 3 + (ret->s[0][0] == '*' || ret->s[1][0] == '*'? 1 : 1) * qr_indel;
486 min1 = min2 = 0x7fffffff; min1_i = -1;
487 for (i = 0; i < 3; ++i) {
489 min2 = min1; min1 = q[i]; min1_i = i;
490 } else if (q[i] < min2) min2 = q[i];
493 ret->q_cns = min2 - min1;
495 if (ret->gt < 2) ret->q_ref = (ret->s[ret->gt][0] == '*')? 0 : q[1-ret->gt] - q[ret->gt] - qr_indel - 3;
496 else ret->q_ref = (ret->s[0][0] == '*')? q[0] - q[2] : q[1] - q[2];
497 if (ret->q_ref < 0) ret->q_ref = 0;