bam2bcf.c

   1 #include <math.h>
   2 #include <stdint.h>
   3 #include "bam.h"
   4 #include "kstring.h"
   5 #include "bam2bcf.h"
   6 #include "errmod.h"
   7 #include "bcftools/bcf.h"
   8
   9 extern  void ks_introsort_uint32_t(size_t n, uint32_t a[]);
  10
  11 #define CALL_ETA 0.03f
  12 #define CALL_MAX 256
  13 #define CALL_DEFTHETA 0.83f
  14 #define DEF_MAPQ 20
  15
  16 #define CAP_DIST 25
  17
  18 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
  19 {
  20         bcf_callaux_t *bca;
  21         if (theta <= 0.) theta = CALL_DEFTHETA;
  22         bca = calloc(1, sizeof(bcf_callaux_t));
  23         bca->capQ = 60;
  24         bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
  25         bca->min_baseQ = min_baseQ;
  26         bca->e = errmod_init(1. - theta);
  27         bca->min_frac = 0.002;
  28         bca->min_support = 1;
  29         return bca;
  30 }
  31
  32 void bcf_call_destroy(bcf_callaux_t *bca)
  33 {
  34         if (bca == 0) return;
  35         errmod_destroy(bca->e);
  36         free(bca->bases); free(bca->inscns); free(bca);
  37 }
  38 /* ref_base is the 4-bit representation of the reference base. It is
  39  * negative if we are looking at an indel. */
  40 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
  41 {
  42     static int *var_pos = NULL, nvar_pos = 0;
  43         int i, n, ref4, is_indel, ori_depth = 0;
  44         memset(r, 0, sizeof(bcf_callret1_t));
  45         if (ref_base >= 0) {
  46                 ref4 = bam_nt16_nt4_table[ref_base];
  47                 is_indel = 0;
  48         } else ref4 = 4, is_indel = 1;
  49         if (_n == 0) return -1;
  50         // enlarge the bases array if necessary
  51         if (bca->max_bases < _n) {
  52                 bca->max_bases = _n;
  53                 kroundup32(bca->max_bases);
  54                 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
  55         }
  56         // fill the bases array
  57         memset(r, 0, sizeof(bcf_callret1_t));
  58         for (i = n = 0; i < _n; ++i) {
  59                 const bam_pileup1_t *p = pl + i;
  60                 int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
  61                 // set base
  62                 if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
  63                 ++ori_depth;
  64                 baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
  65                 seqQ = is_indel? (p->aux>>8&0xff) : 99;
  66                 if (q < bca->min_baseQ) continue;
  67                 if (q > seqQ) q = seqQ;
  68                 mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
  69                 mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
  70                 if (q > mapQ) q = mapQ;
  71                 if (q > 63) q = 63;
  72                 if (q < 4) q = 4;
  73                 if (!is_indel) {
  74                         b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
  75                         b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
  76                         is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
  77                 } else {
  78                         b = p->aux>>16&0x3f;
  79                         is_diff = (b != 0);
  80                 }
  81                 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
  82                 // collect annotations
  83                 if (b < 4) r->qsum[b] += q;
  84                 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
  85                 min_dist = p->b->core.l_qseq - 1 - p->qpos;
  86                 if (min_dist > p->qpos) min_dist = p->qpos;
  87                 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
  88                 r->anno[1<<2|is_diff<<1|0] += baseQ;
  89                 r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
  90                 r->anno[2<<2|is_diff<<1|0] += mapQ;
  91                 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
  92                 r->anno[3<<2|is_diff<<1|0] += min_dist;
  93                 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
  94         }
  95         r->depth = n; r->ori_depth = ori_depth;
  96         // glfgen
  97         errmod_cal(bca->e, n, 5, bca->bases, r->p);
  98
  99     // Calculate the Variant Distance Bias (make it optional?)
 100     if ( nvar_pos < _n ) {
 101         nvar_pos = _n;
 102         var_pos = realloc(var_pos,sizeof(int)*nvar_pos);
 103     }
 104     int alt_dp=0, read_len=0;
 105     for (i=0; i<_n; i++) {
 106         const bam_pileup1_t *p = pl + i;
 107         if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base )
 108             continue;
 109
 110         var_pos[alt_dp] = p->qpos;
 111         if ( (bam1_cigar(p->b)[0]&BAM_CIGAR_MASK)==4 )
 112             var_pos[alt_dp] -= bam1_cigar(p->b)[0]>>BAM_CIGAR_SHIFT;
 113
 114         alt_dp++;
 115         read_len += p->b->core.l_qseq;
 116     }
 117     float mvd=0;
 118     int j;
 119     n=0;
 120     for (i=0; i<alt_dp; i++) {
 121         for (j=0; j<i; j++) {
 122             mvd += abs(var_pos[i] - var_pos[j]);
 123             n++;
 124         }
 125     }
 126     r->mvd[0] = n ? mvd/n : 0;
 127     r->mvd[1] = alt_dp;
 128     r->mvd[2] = alt_dp ? read_len/alt_dp : 0;
 129
 130         return r->depth;
 131 }
 132
 133
 134 void calc_vdb(int n, const bcf_callret1_t *calls, bcf_call_t *call)
 135 {
 136     // Variant distance bias. Samples merged by means of DP-weighted average.
 137
 138     float weight=0, tot_prob=0;
 139
 140     int i;
 141     for (i=0; i<n; i++)
 142     {
 143         int mvd      = calls[i].mvd[0];
 144         int dp       = calls[i].mvd[1];
 145         int read_len = calls[i].mvd[2];
 146
 147         if ( dp<2 ) continue;
 148
 149         float prob = 0;
 150         if ( dp==2 )
 151         {
 152             // Exact formula
 153             prob = (mvd==0) ? 1.0/read_len : (read_len-mvd)*2.0/read_len/read_len;
 154         }
 155         else if ( dp==3 )
 156         {
 157             // Sin, quite accurate approximation
 158             float mu = read_len/2.9;
 159             prob = mvd>2*mu ? 0 : sin(mvd*3.14/2/mu) / (4*mu/3.14);
 160         }
 161         else
 162         {
 163             // Scaled gaussian curve, crude approximation, but behaves well. Using fixed depth for bigger depths.
 164             if ( dp>5 )
 165                 dp = 5;
 166             float sigma2 = (read_len/1.9/(dp+1)) * (read_len/1.9/(dp+1));
 167             float norm   = 1.125*sqrt(2*3.14*sigma2);
 168             float mu     = read_len/2.9;
 169             if ( mvd < mu )
 170                 prob = exp(-(mvd-mu)*(mvd-mu)/2/sigma2)/norm;
 171             else
 172                 prob = exp(-(mvd-mu)*(mvd-mu)/3.125/sigma2)/norm;
 173         }
 174
 175         //fprintf(stderr,"dp=%d mvd=%d read_len=%d -> prob=%f\n", dp,mvd,read_len,prob);
 176         tot_prob += prob*dp;
 177         weight += dp;
 178     }
 179     tot_prob = weight ? tot_prob/weight : 1;
 180     //fprintf(stderr,"prob=%f\n", tot_prob);
 181     call->vdb = tot_prob;
 182 }
 183
 184 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 185 {
 186         int ref4, i, j, qsum[4];
 187         int64_t tmp;
 188         if (ref_base >= 0) {
 189                 call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
 190                 if (ref4 > 4) ref4 = 4;
 191         } else call->ori_ref = -1, ref4 = 0;
 192         // calculate qsum
 193         memset(qsum, 0, 4 * sizeof(int));
 194         for (i = 0; i < n; ++i)
 195                 for (j = 0; j < 4; ++j)
 196                         qsum[j] += calls[i].qsum[j];
 197         for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
 198         // find the top 2 alleles
 199         for (i = 1; i < 4; ++i) // insertion sort
 200                 for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
 201                         tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
 202         // set the reference allele and alternative allele(s)
 203         for (i = 0; i < 5; ++i) call->a[i] = -1;
 204         call->unseen = -1;
 205         call->a[0] = ref4;
 206         for (i = 3, j = 1; i >= 0; --i) {
 207                 if ((qsum[i]&3) != ref4) {
 208                         if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
 209                         else break;
 210                 }
 211         }
 212         if (ref_base >= 0) { // for SNPs, find the "unseen" base
 213                 if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
 214                         call->unseen = j, call->a[j++] = qsum[i]&3;
 215                 call->n_alleles = j;
 216         } else {
 217                 call->n_alleles = j;
 218                 if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
 219         }
 220         // set the PL array
 221         if (call->n < n) {
 222                 call->n = n;
 223                 call->PL = realloc(call->PL, 15 * n);
 224         }
 225         {
 226                 int x, g[15], z;
 227                 double sum_min = 0.;
 228                 x = call->n_alleles * (call->n_alleles + 1) / 2;
 229                 // get the possible genotypes
 230                 for (i = z = 0; i < call->n_alleles; ++i)
 231                         for (j = 0; j <= i; ++j)
 232                                 g[z++] = call->a[j] * 5 + call->a[i];
 233                 for (i = 0; i < n; ++i) {
 234                         uint8_t *PL = call->PL + x * i;
 235                         const bcf_callret1_t *r = calls + i;
 236                         float min = 1e37;
 237                         for (j = 0; j < x; ++j)
 238                                 if (min > r->p[g[j]]) min = r->p[g[j]];
 239                         sum_min += min;
 240                         for (j = 0; j < x; ++j) {
 241                                 int y;
 242                                 y = (int)(r->p[g[j]] - min + .499);
 243                                 if (y > 255) y = 255;
 244                                 PL[j] = y;
 245                         }
 246                 }
 247 //              if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
 248                 call->shift = (int)(sum_min + .499);
 249         }
 250         // combine annotations
 251         memset(call->anno, 0, 16 * sizeof(int));
 252         for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
 253                 call->depth += calls[i].depth;
 254                 call->ori_depth += calls[i].ori_depth;
 255                 for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
 256         }
 257
 258     calc_vdb(n, calls, call);
 259
 260         return 0;
 261 }
 262
 263 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
 264                                  const bcf_callaux_t *bca, const char *ref)
 265 {
 266         extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
 267         kstring_t s;
 268         int i, j;
 269         b->n_smpl = bc->n;
 270         b->tid = tid; b->pos = pos; b->qual = 0;
 271         s.s = b->str; s.m = b->m_str; s.l = 0;
 272         kputc('\0', &s);
 273         if (bc->ori_ref < 0) { // an indel
 274                 // write REF
 275                 kputc(ref[pos], &s);
 276                 for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
 277                 kputc('\0', &s);
 278                 // write ALT
 279                 kputc(ref[pos], &s);
 280                 for (i = 1; i < 4; ++i) {
 281                         if (bc->a[i] < 0) break;
 282                         if (i > 1) {
 283                                 kputc(',', &s); kputc(ref[pos], &s);
 284                         }
 285                         if (bca->indel_types[bc->a[i]] < 0) { // deletion
 286                                 for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
 287                                         kputc(ref[pos+1+j], &s);
 288                         } else { // insertion; cannot be a reference unless a bug
 289                                 char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
 290                                 for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
 291                                         kputc("ACGTN"[(int)inscns[j]], &s);
 292                                 for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
 293                         }
 294                 }
 295                 kputc('\0', &s);
 296         } else { // a SNP
 297                 kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
 298                 for (i = 1; i < 5; ++i) {
 299                         if (bc->a[i] < 0) break;
 300                         if (i > 1) kputc(',', &s);
 301                         kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
 302                 }
 303                 kputc('\0', &s);
 304         }
 305         kputc('\0', &s);
 306         // INFO
 307         if (bc->ori_ref < 0) kputs("INDEL;", &s);
 308         kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
 309         for (i = 0; i < 16; ++i) {
 310                 if (i) kputc(',', &s);
 311                 kputw(bc->anno[i], &s);
 312         }
 313     if ( bc->vdb!=1 )
 314     {
 315         ksprintf(&s, ";VDB=%.4f", bc->vdb);
 316     }
 317         kputc('\0', &s);
 318         // FMT
 319         kputs("PL", &s);
 320         if (bcr) {
 321                 kputs(":DP", &s);
 322                 if (is_SP) kputs(":SP", &s);
 323         }
 324         kputc('\0', &s);
 325         b->m_str = s.m; b->str = s.s; b->l_str = s.l;
 326         bcf_sync(b);
 327         memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
 328         if (bcr) {
 329                 uint16_t *dp = (uint16_t*)b->gi[1].data;
 330                 int32_t *sp = is_SP? b->gi[2].data : 0;
 331                 for (i = 0; i < bc->n; ++i) {
 332                         bcf_callret1_t *p = bcr + i;
 333                         dp[i] = p->depth < 0xffff? p->depth : 0xffff;
 334                         if (is_SP) {
 335                                 if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
 336                                         || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
 337                                 {
 338                                         sp[i] = 0;
 339                                 } else {
 340                                         double left, right, two;
 341                                         int x;
 342                                         kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
 343                                         x = (int)(-4.343 * log(two) + .499);
 344                                         if (x > 255) x = 255;
 345                                         sp[i] = x;
 346                                 }
 347                         }
 348                 }
 349         }
 350         return 0;
 351 }