bam2bcf.c

   1 #include <math.h>
   2 #include <stdint.h>
   3 #include "bam.h"
   4 #include "kstring.h"
   5 #include "bam2bcf.h"
   6 #include "bcftools/bcf.h"
   7
   8 extern  void ks_introsort_uint32_t(size_t n, uint32_t a[]);
   9
  10 #define CALL_ETA 0.03f
  11 #define CALL_MAX 256
  12 #define CALL_DEFTHETA 0.83f
  13
  14 #define CAP_DIST 25
  15
  16 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
  17 {
  18         bcf_callaux_t *bca;
  19         if (theta <= 0.) theta = CALL_DEFTHETA;
  20         bca = calloc(1, sizeof(bcf_callaux_t));
  21         bca->capQ = 60;
  22         bca->openQ = 40;
  23         bca->extQ = 20;
  24         bca->tandemQ = 100;
  25         bca->min_baseQ = min_baseQ;
  26         bca->e = errmod_init(1. - theta);
  27         return bca;
  28 }
  29
  30 void bcf_call_destroy(bcf_callaux_t *bca)
  31 {
  32         if (bca == 0) return;
  33         errmod_destroy(bca->e);
  34         free(bca->bases); free(bca);
  35 }
  36
  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)
  38 {
  39         int i, n, ref4;
  40         memset(r, 0, sizeof(bcf_callret1_t));
  41         ref4 = bam_nt16_nt4_table[ref_base];
  42         if (_n == 0) return -1;
  43
  44         // enlarge the bases array if necessary
  45         if (bca->max_bases < _n) {
  46                 bca->max_bases = _n;
  47                 kroundup32(bca->max_bases);
  48                 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
  49         }
  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;
  55                 // set base
  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;
  61                 if (q > 63) q = 63;
  62                 if (q < 4) q = 4;
  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
  67                 r->qsum[b] += q;
  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;
  79         }
  80         r->depth = n;
  81         // glfgen
  82         errmod_cal(bca->e, n, 5, bca->bases, r->p);
  83         return r->depth;
  84 }
  85
  86 int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r)
  87 {
  88         int i, n, n_ins, n_del;
  89         memset(r, 0, sizeof(bcf_callret1_t));
  90         if (_n == 0) return -1;
  91
  92         // enlarge the bases array if necessary
  93         if (bca->max_bases < _n) {
  94                 bca->max_bases = _n;
  95                 kroundup32(bca->max_bases);
  96                 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
  97         }
  98         // fill the bases array
  99         memset(r, 0, sizeof(bcf_callret1_t));
 100         r->indelreg = 10000;
 101         n_ins = n_del = 0;
 102         for (i = n = 0; i < _n; ++i) {
 103                 const bam_pileup1_t *p = pl + i;
 104                 int q, b, mapQ, indelQ, is_diff, min_dist;
 105                 if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
 106                 { // compute indel (base) quality
 107                         // this can be made more efficient, but realignment is the bottleneck anyway
 108                         int j, k, x, y, op, len = 0, max_left, max_rght, seqQ, indelreg;
 109                         bam1_core_t *c = &p->b->core;
 110                         uint32_t *cigar = bam1_cigar(p->b);
 111                         uint8_t *qual = bam1_qual(p->b);
 112                         for (k = y = 0, x = c->pos; k < c->n_cigar && y <= p->qpos; ++k) {
 113                                 op = cigar[k]&0xf;
 114                                 len = cigar[k]>>4;
 115                                 if (op == BAM_CMATCH) {
 116                                         if (pos > x && pos < x + len) break;
 117                                         x += len; y += len;
 118                                 } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += len;
 119                                 else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += len;
 120                         }
 121                         if (k == c->n_cigar) continue; // this actually should not happen
 122                         max_left = max_rght = 0; indelreg = 0;
 123                         if (pos == x + len - 1 && k+2 < c->n_cigar && ((cigar[k+1]&0xf) == BAM_CINS || (cigar[k+1]&0xf) == BAM_CDEL)
 124                                 && (cigar[k+2]&0xf) == BAM_CMATCH)
 125                         {
 126                                 for (j = y; j < y + len; ++j)
 127                                         if (max_left < qual[j]) max_left = qual[j];
 128                                 if ((cigar[k+1]&0xf) == BAM_CINS) y += cigar[k+1]>>4;
 129                                 else x += cigar[k+1]>>4;
 130                                 op = cigar[k+2]&0xf; len = cigar[k+2]>>4;
 131                                 for (j = y; j < y + len; ++j) {
 132                                         if (max_rght < qual[j]) max_rght = qual[j];
 133                                         if (qual[j] > BAM2BCF_INDELREG_THRES && indelreg == 0)
 134                                                 indelreg = j - y + 1;
 135                                 }
 136                                 if (r->indelreg > indelreg) r->indelreg = indelreg;
 137                         } else {
 138                                 for (j = y; j <= p->qpos; ++j)
 139                                         if (max_left < qual[j]) max_left = qual[j];
 140                                 for (j = p->qpos + 1; j < y + len; ++j)
 141                                         if (max_rght < qual[j]) max_rght = qual[j];
 142
 143                         }
 144                         indelQ = max_left < max_rght? max_left : max_rght;
 145                         // estimate the sequencing error rate
 146                         seqQ = bca->openQ;
 147                         if (p->indel != 0) seqQ += bca->extQ * (abs(p->indel) - 1); // FIXME: better to model homopolymer
 148                         if (p->indel > 0) {
 149                                 ++n_ins; r->ins_len += p->indel;
 150                         } else if (p->indel < 0) {
 151                                 ++n_del; r->del_len += -p->indel;
 152                         }
 153                         if (p->indel != 0) { // a different model for tandem repeats
 154                                 uint8_t *seq = bam1_seq(p->b);
 155                                 int tandemQ, qb = bam1_seqi(seq, p->qpos), l;
 156                                 for (j = p->qpos + 1; j < c->l_qseq; ++j)
 157                                         if (qb != bam1_seqi(seq, j)) break;
 158                                 l = j;
 159                                 for (j = (int)p->qpos - 1; j >= 0; --j)
 160                                         if (qb != bam1_seqi(seq, j)) break;
 161                                 l = l - (j + 1);
 162                                 tandemQ = (int)((double)(abs(p->indel)) / l * bca->tandemQ + .499);
 163                                 if (seqQ > tandemQ) seqQ = tandemQ;
 164                         }
 165 //                      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);
 166                         if (indelQ > seqQ) indelQ = seqQ;
 167                         q = indelQ;
 168                 }
 169                 if (q < bca->min_baseQ) continue;
 170                 mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
 171                 if (q > mapQ) q = mapQ;
 172                 if (q > 63) q = 63;
 173                 if (q < 4) q = 4;
 174                 b = p->indel? 1 : 0;
 175                 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
 176                 // collect annotations
 177                 r->qsum[b] += q;
 178                 is_diff = b;
 179                 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
 180                 min_dist = p->b->core.l_qseq - 1 - p->qpos;
 181                 if (min_dist > p->qpos) min_dist = p->qpos;
 182                 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
 183                 r->anno[1<<2|is_diff<<1|0] += indelQ;
 184                 r->anno[1<<2|is_diff<<1|1] += indelQ * indelQ;
 185                 r->anno[2<<2|is_diff<<1|0] += mapQ;
 186                 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
 187                 r->anno[3<<2|is_diff<<1|0] += min_dist;
 188                 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
 189         }
 190         r->depth = n;
 191         r->ins_len = n_ins? r->ins_len / n_ins : 0;
 192         r->del_len = n_del? r->del_len / n_del : 0;
 193         if (r->indelreg >= 10000) r->indelreg = 0;
 194         // glfgen
 195         errmod_cal(bca->e, n, 2, bca->bases, r->p);
 196         return r->depth;
 197 }
 198
 199 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 200 {
 201         int ref4, i, j, qsum[4];
 202         int64_t tmp;
 203         call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
 204         call->ins_len = call->del_len = 0; call->indelreg = 0;
 205         if (ref4 > 4) ref4 = 4;
 206         // calculate qsum
 207         memset(qsum, 0, 4 * sizeof(int));
 208         for (i = 0; i < n; ++i)
 209                 for (j = 0; j < 4; ++j)
 210                         qsum[j] += calls[i].qsum[j];
 211         for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
 212         // find the top 2 alleles
 213         for (i = 1; i < 4; ++i) // insertion sort
 214                 for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
 215                         tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
 216         // set the reference allele and alternative allele(s)
 217         for (i = 0; i < 5; ++i) call->a[i] = -1;
 218         call->unseen = -1;
 219         call->a[0] = ref4;
 220         for (i = 3, j = 1; i >= 0; --i) {
 221                 if ((qsum[i]&3) != ref4) {
 222                         if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
 223                         else break;
 224                 }
 225         }
 226         if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
 227                 call->unseen = j, call->a[j++] = qsum[i]&3;
 228         call->n_alleles = j;
 229         // set the PL array
 230         if (call->n < n) {
 231                 call->n = n;
 232                 call->PL = realloc(call->PL, 15 * n);
 233         }
 234         {
 235                 int x, g[15], z;
 236                 double sum_min = 0.;
 237                 x = call->n_alleles * (call->n_alleles + 1) / 2;
 238                 // get the possible genotypes
 239                 for (i = z = 0; i < call->n_alleles; ++i)
 240                         for (j = i; j < call->n_alleles; ++j)
 241                                 g[z++] = call->a[i] * 5 + call->a[j];
 242                 for (i = 0; i < n; ++i) {
 243                         uint8_t *PL = call->PL + x * i;
 244                         const bcf_callret1_t *r = calls + i;
 245                         float min = 1e37;
 246                         for (j = 0; j < x; ++j)
 247                                 if (min > r->p[g[j]]) min = r->p[g[j]];
 248                         sum_min += min;
 249                         for (j = 0; j < x; ++j) {
 250                                 int y;
 251                                 y = (int)(r->p[g[j]] - min + .499);
 252                                 if (y > 255) y = 255;
 253                                 PL[j] = y;
 254                         }
 255                 }
 256                 call->shift = (int)(sum_min + .499);
 257         }
 258         // combine annotations
 259         memset(call->anno, 0, 16 * sizeof(int));
 260         for (i = call->depth = 0, tmp = 0; i < n; ++i) {
 261                 call->depth += calls[i].depth;
 262                 for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
 263         }
 264         return 0;
 265 }
 266
 267 int bcf_call_combine_gap(int n, const bcf_callret1_t *calls, bcf_call_t *call)
 268 {
 269         int i, j, n_ins, n_del;
 270         // combine annotations
 271         call->ori_ref = 4;
 272         memset(call->anno, 0, 16 * sizeof(int));
 273         call->ins_len = call->del_len = 0; call->indelreg = 10000;
 274         for (i = call->depth = 0, n_ins = n_del = 0; i < n; ++i) {
 275                 const bcf_callret1_t *r = calls + i;
 276                 if (r->depth > 0) {
 277                         call->depth += r->depth;
 278                         if (r->ins_len > 0) {
 279                                 call->ins_len += r->ins_len;
 280                                 ++n_ins;
 281                         }
 282                         if (r->del_len > 0) {
 283                                 call->del_len += r->del_len;
 284                                 ++n_del;
 285                         }
 286                         if (r->indelreg > 0 && call->indelreg > r->indelreg)
 287                                 call->indelreg = r->indelreg;
 288                         for (j = 0; j < 16; ++j) call->anno[j] += r->anno[j];
 289                 }
 290         }
 291         if (call->depth == 0) return 0; // no indels
 292         call->ins_len = n_ins? call->ins_len / n_ins : 0;
 293         call->del_len = n_del? call->del_len / n_del : 0;
 294         //
 295         for (i = 0; i < 5; ++i) call->a[i] = -1;
 296         call->a[0] = 0; call->a[1] = 1;
 297         call->unseen = -1;
 298         call->n_alleles = 2;
 299         // set the PL array
 300         if (call->n < n) {
 301                 call->n = n;
 302                 call->PL = realloc(call->PL, 15 * n);
 303         }
 304         {
 305                 int g[3];
 306                 double sum_min = 0.;
 307                 g[0] = 0; g[1] = 1; g[2] = 3;
 308                 for (i = 0; i < n; ++i) {
 309                         uint8_t *PL = call->PL + 3 * i;
 310                         const bcf_callret1_t *r = calls + i;
 311                         float min = 1e37;
 312                         for (j = 0; j < 3; ++j)
 313                                 if (min > r->p[g[j]]) min = r->p[g[j]];
 314                         sum_min += min;
 315                         for (j = 0; j < 3; ++j) {
 316                                 int y;
 317                                 y = (int)(r->p[g[j]] - min + .499);
 318                                 if (y > 255) y = 255;
 319                                 PL[j] = y;
 320                         }
 321                 }
 322                 call->shift = (int)(sum_min + .499);
 323         }
 324         return 0;
 325 }
 326
 327 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
 328 {
 329         extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
 330         kstring_t s;
 331         int i;
 332         b->n_smpl = bc->n;
 333         b->tid = tid; b->pos = pos; b->qual = 0;
 334         s.s = b->str; s.m = b->m_str; s.l = 0;
 335         kputc('\0', &s);
 336         if (bc->ins_len > 0 || bc->del_len > 0) { // an indel
 337                 for (i = 0; i < bc->indelreg; ++i) kputc('N', &s);
 338                 kputc('\0', &s);
 339                 if (bc->ins_len > 0 && bc->del_len > 0) kputs("<INDEL>", &s);
 340                 else if (bc->ins_len > 0) kputs("<INS>", &s);
 341                 else if (bc->del_len > 0) kputs("<DEL>", &s);
 342         } else { // SNP
 343                 kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
 344                 for (i = 1; i < 5; ++i) {
 345                         if (bc->a[i] < 0) break;
 346                         if (i > 1) kputc(',', &s);
 347                         kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
 348                 }
 349         }
 350         kputc('\0', &s);
 351         kputc('\0', &s);
 352         // INFO
 353         kputs("I16=", &s);
 354         for (i = 0; i < 16; ++i) {
 355                 if (i) kputc(',', &s);
 356                 kputw(bc->anno[i], &s);
 357         }
 358         kputc('\0', &s);
 359         // FMT
 360         kputs("PL", &s);
 361         if (bcr) {
 362                 kputs(":DP", &s);
 363                 if (is_SP) kputs(":SP", &s);
 364         }
 365         kputc('\0', &s);
 366         b->m_str = s.m; b->str = s.s; b->l_str = s.l;
 367         bcf_sync(b);
 368         memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
 369         if (bcr) {
 370                 uint16_t *dp = (uint16_t*)b->gi[1].data;
 371                 uint8_t *sp = is_SP? b->gi[2].data : 0;
 372                 for (i = 0; i < bc->n; ++i) {
 373                         bcf_callret1_t *p = bcr + i;
 374                         dp[i] = p->depth < 0xffff? p->depth : 0xffff;
 375                         if (is_SP) {
 376                                 if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
 377                                         || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
 378                                 {
 379                                         sp[i] = 0;
 380                                 } else {
 381                                         double left, right, two;
 382                                         int x;
 383                                         kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
 384                                         x = (int)(-4.343 * log(two) + .499);
 385                                         if (x > 255) x = 255;
 386                                         sp[i] = x;
 387                                 }
 388                         }
 389                 }
 390         }
 391         return 0;
 392 }