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         int i, n, ref4, is_indel, ori_depth = 0;
  43         memset(r, 0, sizeof(bcf_callret1_t));
  44         if (ref_base >= 0) {
  45                 ref4 = bam_nt16_nt4_table[ref_base];
  46                 is_indel = 0;
  47         } else ref4 = 4, is_indel = 1;
  48         if (_n == 0) return -1;
  49         // enlarge the bases array if necessary
  50         if (bca->max_bases < _n) {
  51                 bca->max_bases = _n;
  52                 kroundup32(bca->max_bases);
  53                 bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
  54         }
  55         // fill the bases array
  56         memset(r, 0, sizeof(bcf_callret1_t));
  57         for (i = n = 0; i < _n; ++i) {
  58                 const bam_pileup1_t *p = pl + i;
  59                 int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
  60                 // set base
  61                 if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
  62                 ++ori_depth;
  63                 baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
  64                 seqQ = is_indel? (p->aux>>8&0xff) : 99;
  65                 if (q < bca->min_baseQ) continue;
  66                 if (q > seqQ) q = seqQ;
  67                 mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
  68                 mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
  69                 if (q > mapQ) q = mapQ;
  70                 if (q > 63) q = 63;
  71                 if (q < 4) q = 4;
  72                 if (!is_indel) {
  73                         b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
  74                         b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
  75                         is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
  76                 } else {
  77                         b = p->aux>>16&0x3f;
  78                         is_diff = (b != 0);
  79                 }
  80                 bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
  81                 // collect annotations
  82                 if (b < 4) r->qsum[b] += q;
  83                 ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
  84                 min_dist = p->b->core.l_qseq - 1 - p->qpos;
  85                 if (min_dist > p->qpos) min_dist = p->qpos;
  86                 if (min_dist > CAP_DIST) min_dist = CAP_DIST;
  87                 r->anno[1<<2|is_diff<<1|0] += baseQ;
  88                 r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
  89                 r->anno[2<<2|is_diff<<1|0] += mapQ;
  90                 r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
  91                 r->anno[3<<2|is_diff<<1|0] += min_dist;
  92                 r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
  93         }
  94         r->depth = n; r->ori_depth = ori_depth;
  95         // glfgen
  96         errmod_cal(bca->e, n, 5, bca->bases, r->p);
  97         return r->depth;
  98 }
  99
 100 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 101 {
 102         int ref4, i, j, qsum[4];
 103         int64_t tmp;
 104         if (ref_base >= 0) {
 105                 call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
 106                 if (ref4 > 4) ref4 = 4;
 107         } else call->ori_ref = -1, ref4 = 0;
 108         // calculate qsum
 109         memset(qsum, 0, 4 * sizeof(int));
 110         for (i = 0; i < n; ++i)
 111                 for (j = 0; j < 4; ++j)
 112                         qsum[j] += calls[i].qsum[j];
 113         for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
 114         // find the top 2 alleles
 115         for (i = 1; i < 4; ++i) // insertion sort
 116                 for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
 117                         tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
 118         // set the reference allele and alternative allele(s)
 119         for (i = 0; i < 5; ++i) call->a[i] = -1;
 120         call->unseen = -1;
 121         call->a[0] = ref4;
 122         for (i = 3, j = 1; i >= 0; --i) {
 123                 if ((qsum[i]&3) != ref4) {
 124                         if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
 125                         else break;
 126                 }
 127         }
 128         if (ref_base >= 0) { // for SNPs, find the "unseen" base
 129                 if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
 130                         call->unseen = j, call->a[j++] = qsum[i]&3;
 131                 call->n_alleles = j;
 132         } else {
 133                 call->n_alleles = j;
 134                 if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
 135         }
 136         // set the PL array
 137         if (call->n < n) {
 138                 call->n = n;
 139                 call->PL = realloc(call->PL, 15 * n);
 140         }
 141         {
 142                 int x, g[15], z;
 143                 double sum_min = 0.;
 144                 x = call->n_alleles * (call->n_alleles + 1) / 2;
 145                 // get the possible genotypes
 146                 for (i = z = 0; i < call->n_alleles; ++i)
 147                         for (j = 0; j <= i; ++j)
 148                                 g[z++] = call->a[j] * 5 + call->a[i];
 149                 for (i = 0; i < n; ++i) {
 150                         uint8_t *PL = call->PL + x * i;
 151                         const bcf_callret1_t *r = calls + i;
 152                         float min = 1e37;
 153                         for (j = 0; j < x; ++j)
 154                                 if (min > r->p[g[j]]) min = r->p[g[j]];
 155                         sum_min += min;
 156                         for (j = 0; j < x; ++j) {
 157                                 int y;
 158                                 y = (int)(r->p[g[j]] - min + .499);
 159                                 if (y > 255) y = 255;
 160                                 PL[j] = y;
 161                         }
 162                 }
 163 //              if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
 164                 call->shift = (int)(sum_min + .499);
 165         }
 166         // combine annotations
 167         memset(call->anno, 0, 16 * sizeof(int));
 168         for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
 169                 call->depth += calls[i].depth;
 170                 call->ori_depth += calls[i].ori_depth;
 171                 for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
 172         }
 173         return 0;
 174 }
 175
 176 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
 177                                  const bcf_callaux_t *bca, const char *ref)
 178 {
 179         extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
 180         kstring_t s;
 181         int i, j;
 182         b->n_smpl = bc->n;
 183         b->tid = tid; b->pos = pos; b->qual = 0;
 184         s.s = b->str; s.m = b->m_str; s.l = 0;
 185         kputc('\0', &s);
 186         if (bc->ori_ref < 0) { // an indel
 187                 // write REF
 188                 kputc(ref[pos], &s);
 189                 for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
 190                 kputc('\0', &s);
 191                 // write ALT
 192                 kputc(ref[pos], &s);
 193                 for (i = 1; i < 4; ++i) {
 194                         if (bc->a[i] < 0) break;
 195                         if (i > 1) {
 196                                 kputc(',', &s); kputc(ref[pos], &s);
 197                         }
 198                         if (bca->indel_types[bc->a[i]] < 0) { // deletion
 199                                 for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
 200                                         kputc(ref[pos+1+j], &s);
 201                         } else { // insertion; cannot be a reference unless a bug
 202                                 char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
 203                                 for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
 204                                         kputc("ACGTN"[(int)inscns[j]], &s);
 205                                 for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
 206                         }
 207                 }
 208                 kputc('\0', &s);
 209         } else { // a SNP
 210                 kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
 211                 for (i = 1; i < 5; ++i) {
 212                         if (bc->a[i] < 0) break;
 213                         if (i > 1) kputc(',', &s);
 214                         kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
 215                 }
 216                 kputc('\0', &s);
 217         }
 218         kputc('\0', &s);
 219         // INFO
 220         if (bc->ori_ref < 0) kputs("INDEL;", &s);
 221         kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
 222         for (i = 0; i < 16; ++i) {
 223                 if (i) kputc(',', &s);
 224                 kputw(bc->anno[i], &s);
 225         }
 226         kputc('\0', &s);
 227         // FMT
 228         kputs("PL", &s);
 229         if (bcr) {
 230                 kputs(":DP", &s);
 231                 if (is_SP) kputs(":SP", &s);
 232         }
 233         kputc('\0', &s);
 234         b->m_str = s.m; b->str = s.s; b->l_str = s.l;
 235         bcf_sync(b);
 236         memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
 237         if (bcr) {
 238                 uint16_t *dp = (uint16_t*)b->gi[1].data;
 239                 uint8_t *sp = is_SP? b->gi[2].data : 0;
 240                 for (i = 0; i < bc->n; ++i) {
 241                         bcf_callret1_t *p = bcr + i;
 242                         dp[i] = p->depth < 0xffff? p->depth : 0xffff;
 243                         if (is_SP) {
 244                                 if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
 245                                         || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
 246                                 {
 247                                         sp[i] = 0;
 248                                 } else {
 249                                         double left, right, two;
 250                                         int x;
 251                                         kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
 252                                         x = (int)(-4.343 * log(two) + .499);
 253                                         if (x > 255) x = 255;
 254                                         sp[i] = x;
 255                                 }
 256                         }
 257                 }
 258         }
 259         return 0;
 260 }