X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=7947a31f5d2a627fe7f2651f60cbb597048b715c;hb=4b7090735c74dfb91ab6cb59c588250c0eeea974;hp=08120fc46c2a3902e01582b45de0659d4b333eb6;hpb=d062f8f3ca3f897b7a95c81e76d05e94b1d39877;p=samtools.git diff --git a/bam2bcf.c b/bam2bcf.c index 08120fc..7947a31 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -1,5 +1,6 @@ #include #include +#include #include "bam.h" #include "kstring.h" #include "bam2bcf.h" @@ -11,6 +12,7 @@ extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); #define CALL_ETA 0.03f #define CALL_MAX 256 #define CALL_DEFTHETA 0.83f +#define DEF_MAPQ 20 #define CAP_DIST 25 @@ -25,13 +27,49 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ) bca->e = errmod_init(1. - theta); bca->min_frac = 0.002; bca->min_support = 1; - return bca; + bca->per_sample_flt = 0; + bca->npos = 100; + bca->ref_pos = calloc(bca->npos, sizeof(int)); + bca->alt_pos = calloc(bca->npos, sizeof(int)); + return bca; +} + + +static int get_position(const bam_pileup1_t *p, int *len) +{ + int icig, n_tot_bases = 0, iread = 0, edist = p->qpos + 1; + for (icig=0; icigb->core.n_cigar; icig++) + { + // Conversion from uint32_t to MIDNSHP + // 0123456 + // MIDNSHP + int cig = bam1_cigar(p->b)[icig] & BAM_CIGAR_MASK; + int ncig = bam1_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT; + if ( cig==0 ) + { + n_tot_bases += ncig; + iread += ncig; + } + else if ( cig==1 ) + { + n_tot_bases += ncig; + iread += ncig; + } + else if ( cig==4 ) + { + iread += ncig; + if ( iread<=p->qpos ) edist -= ncig; + } + } + *len = n_tot_bases; + return edist; } void bcf_call_destroy(bcf_callaux_t *bca) { if (bca == 0) return; errmod_destroy(bca->e); + if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; } free(bca->bases); free(bca->inscns); free(bca); } /* ref_base is the 4-bit representation of the reference base. It is @@ -52,8 +90,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); } // fill the bases array - memset(r, 0, sizeof(bcf_callret1_t)); - for (i = n = 0; i < _n; ++i) { + for (i = n = r->n_supp = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; int q, b, mapQ, baseQ, is_diff, min_dist, seqQ; // set base @@ -63,7 +100,8 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t seqQ = is_indel? (p->aux>>8&0xff) : 99; if (q < bca->min_baseQ) continue; if (q > seqQ) q = seqQ; - mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ; + mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255 + mapQ = mapQ < bca->capQ? mapQ : bca->capQ; if (q > mapQ) q = mapQ; if (q > 63) q = 63; if (q < 4) q = 4; @@ -75,9 +113,10 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t b = p->aux>>16&0x3f; is_diff = (b != 0); } + if (is_diff) ++r->n_supp; bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b; // collect annotations - r->qsum[b] += q; + if (b < 4) r->qsum[b] += q; ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)]; min_dist = p->b->core.l_qseq - 1 - p->qpos; if (min_dist > p->qpos) min_dist = p->qpos; @@ -88,6 +127,14 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ; r->anno[3<<2|is_diff<<1|0] += min_dist; r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist; + + // collect read positions for ReadPosBias + int len, pos = get_position(p, &len); + int epos = (double)pos/(len+1) * bca->npos; + if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base ) + bca->ref_pos[epos]++; + else + bca->alt_pos[epos]++; } r->depth = n; r->ori_depth = ori_depth; // glfgen @@ -95,7 +142,148 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t return r->depth; } -int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call) +double mann_whitney_1947(int n, int m, int U) +{ + if (U<0) return 0; + if (n==0||m==0) return U==0 ? 1 : 0; + return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U); +} + +void calc_ReadPosBias(bcf_callaux_t *bca, bcf_call_t *call) +{ + int i, nref = 0, nalt = 0; + unsigned long int U = 0; + for (i=0; inpos; i++) + { + nref += bca->ref_pos[i]; + nalt += bca->alt_pos[i]; + U += nref*bca->alt_pos[i]; + bca->ref_pos[i] = 0; + bca->alt_pos[i] = 0; + } +#if 0 +//todo + double var = 0, avg = (double)(nref+nalt)/bca->npos; + for (i=0; inpos; i++) + { + double ediff = bca->ref_pos[i] + bca->alt_pos[i] - avg; + var += ediff*ediff; + bca->ref_pos[i] = 0; + bca->alt_pos[i] = 0; + } + call->read_pos.avg = avg; + call->read_pos.var = sqrt(var/bca->npos); + call->read_pos.dp = nref+nalt; +#endif + if ( !nref || !nalt ) + { + call->read_pos_bias = -1; + return; + } + + if ( nref>=8 || nalt>=8 ) + { + // normal approximation + double mean = ((double)nref*nalt+1.0)/2.0; + double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0; + double z = (U-mean)/sqrt(var2); + call->read_pos_bias = z; + //fprintf(stderr,"nref=%d nalt=%d U=%ld mean=%e var=%e zval=%e\n", nref,nalt,U,mean,sqrt(var2),call->read_pos_bias); + } + else + { + double p = mann_whitney_1947(nalt,nref,U); + // biased form claimed by GATK to behave better empirically + // double var2 = (1.0+1.0/(nref+nalt+1.0))*(double)nref*nalt*(nref+nalt+1.0)/12.0; + double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0; + double z; + if ( p >= 1./sqrt(var2*2*M_PI) ) z = 0; // equal to mean + else + { + if ( U >= nref*nalt/2. ) z = sqrt(-2*log(sqrt(var2*2*M_PI)*p)); + else z = -sqrt(-2*log(sqrt(var2*2*M_PI)*p)); + } + call->read_pos_bias = z; + //fprintf(stderr,"nref=%d nalt=%d U=%ld p=%e var2=%e zval=%e\n", nref,nalt,U, p,var2,call->read_pos_bias); + } +} + +float mean_diff_to_prob(float mdiff, int dp, int readlen) +{ + if ( dp==2 ) + { + if ( mdiff==0 ) + return (2.0*readlen + 4.0*(readlen-1.0))/((float)readlen*readlen); + else + return 8.0*(readlen - 4.0*mdiff)/((float)readlen*readlen); + } + + // This is crude empirical approximation and is not very accurate for + // shorter read lengths (<100bp). There certainly is a room for + // improvement. + const float mv[24][2] = { {0,0}, {0,0}, {0,0}, + { 9.108, 4.934}, { 9.999, 3.991}, {10.273, 3.485}, {10.579, 3.160}, + {10.828, 2.889}, {11.014, 2.703}, {11.028, 2.546}, {11.244, 2.391}, + {11.231, 2.320}, {11.323, 2.138}, {11.403, 2.123}, {11.394, 1.994}, + {11.451, 1.928}, {11.445, 1.862}, {11.516, 1.815}, {11.560, 1.761}, + {11.544, 1.728}, {11.605, 1.674}, {11.592, 1.652}, {11.674, 1.613}, + {11.641, 1.570} }; + + float m, v; + if ( dp>=24 ) + { + m = readlen/8.; + if (dp>100) dp = 100; + v = 1.476/(0.182*pow(dp,0.514)); + v = v*(readlen/100.); + } + else + { + m = mv[dp][0]; + v = mv[dp][1]; + m = m*readlen/100.; + v = v*readlen/100.; + v *= 1.2; // allow more variability + } + return 1.0/(v*sqrt(2*M_PI)) * exp(-0.5*((mdiff-m)/v)*((mdiff-m)/v)); +} + +void calc_vdb(bcf_callaux_t *bca, bcf_call_t *call) +{ + int i, dp = 0; + float mean_pos = 0, mean_diff = 0; + for (i=0; inpos; i++) + { + if ( !bca->alt_pos[i] ) continue; + dp += bca->alt_pos[i]; + int j = inpos/2 ? i : bca->npos - i; + mean_pos += bca->alt_pos[i]*j; + } + if ( dp<2 ) + { + call->vdb = -1; + return; + } + mean_pos /= dp; + for (i=0; inpos; i++) + { + if ( !bca->alt_pos[i] ) continue; + int j = inpos/2 ? i : bca->npos - i; + mean_diff += bca->alt_pos[i] * fabs(j - mean_pos); + } + mean_diff /= dp; + call->vdb = mean_diff_to_prob(mean_diff, dp, bca->npos); +} + +/** + * bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles + * @n: number of samples + * @calls: each sample's calls + * @bca: auxiliary data structure for holding temporary values + * @ref_base: the reference base + * @call: filled with the annotations + */ +int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call) { int ref4, i, j, qsum[4]; int64_t tmp; @@ -108,6 +296,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, for (i = 0; i < n; ++i) for (j = 0; j < 4; ++j) qsum[j] += calls[i].qsum[j]; + int qsum_tot=0; + for (j=0; j<4; j++) { qsum_tot += qsum[j]; call->qsum[j] = 0; } for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j; // find the top 2 alleles for (i = 1; i < 4; ++i) // insertion sort @@ -119,9 +309,15 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, call->a[0] = ref4; for (i = 3, j = 1; i >= 0; --i) { if ((qsum[i]&3) != ref4) { - if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3; + if (qsum[i]>>2 != 0) + { + if ( j<4 ) call->qsum[j] = (float)(qsum[i]>>2)/qsum_tot; // ref N can make j>=4 + call->a[j++] = qsum[i]&3; + } else break; } + else + call->qsum[0] = (float)(qsum[i]>>2)/qsum_tot; } if (ref_base >= 0) { // for SNPs, find the "unseen" base if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0) @@ -142,8 +338,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, x = call->n_alleles * (call->n_alleles + 1) / 2; // get the possible genotypes for (i = z = 0; i < call->n_alleles; ++i) - for (j = i; j < call->n_alleles; ++j) - g[z++] = call->a[i] * 5 + call->a[j]; + for (j = 0; j <= i; ++j) + g[z++] = call->a[j] * 5 + call->a[i]; for (i = 0; i < n; ++i) { uint8_t *PL = call->PL + x * i; const bcf_callret1_t *r = calls + i; @@ -168,10 +364,14 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, call->ori_depth += calls[i].ori_depth; for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j]; } + + calc_vdb(bca, call); + calc_ReadPosBias(bca, call); + return 0; } -int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP, +int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref) { extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); @@ -215,30 +415,39 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc } kputc('\0', &s); // INFO - if (bc->ori_ref < 0) kputs("INDEL;", &s); + if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IDV=%d;IMF=%f;", bca->max_support, bca->max_frac); kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s); for (i = 0; i < 16; ++i) { if (i) kputc(',', &s); kputw(bc->anno[i], &s); } + //ksprintf(&s,";RPS=%d,%f,%f", bc->read_pos.dp,bc->read_pos.avg,bc->read_pos.var); + ksprintf(&s,";QS=%f,%f,%f,%f", bc->qsum[0],bc->qsum[1],bc->qsum[2],bc->qsum[3]); + if (bc->vdb != -1) + ksprintf(&s, ";VDB=%e", bc->vdb); + if (bc->read_pos_bias != -1 ) + ksprintf(&s, ";RPB=%e", bc->read_pos_bias); kputc('\0', &s); // FMT kputs("PL", &s); - if (bcr) { - kputs(":DP", &s); - if (is_SP) kputs(":SP", &s); + if (bcr && fmt_flag) { + if (fmt_flag & B2B_FMT_DP) kputs(":DP", &s); + if (fmt_flag & B2B_FMT_DV) kputs(":DV", &s); + if (fmt_flag & B2B_FMT_SP) kputs(":SP", &s); } kputc('\0', &s); b->m_str = s.m; b->str = s.s; b->l_str = s.l; bcf_sync(b); memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n); - if (bcr) { - uint16_t *dp = (uint16_t*)b->gi[1].data; - uint8_t *sp = is_SP? b->gi[2].data : 0; + if (bcr && fmt_flag) { + uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0; + uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0; + int32_t *sp = (fmt_flag & B2B_FMT_SP)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0; for (i = 0; i < bc->n; ++i) { bcf_callret1_t *p = bcr + i; - dp[i] = p->depth < 0xffff? p->depth : 0xffff; - if (is_SP) { + if (dp) dp[i] = p->depth < 0xffff? p->depth : 0xffff; + if (dv) dv[i] = p->n_supp < 0xffff? p->n_supp : 0xffff; + if (sp) { if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2 || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2) {