X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=340b10b8ff2ebfc1807af7f2c3b30b35a3dade3e;hb=941fbbbf695efff2c78765d8d0c415ae19b516a1;hp=ab5bfcd20d4a6233109821846842d9996aab93a9;hpb=df7cadac556f302bdd0bc48c235c2b61b699dfe1;p=samtools.git diff --git a/bam2bcf.c b/bam2bcf.c index ab5bfcd..340b10b 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -1,8 +1,10 @@ #include #include +#include #include "bam.h" #include "kstring.h" #include "bam2bcf.h" +#include "errmod.h" #include "bcftools/bcf.h" extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); @@ -10,6 +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 @@ -19,28 +22,67 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ) if (theta <= 0.) theta = CALL_DEFTHETA; bca = calloc(1, sizeof(bcf_callaux_t)); bca->capQ = 60; - bca->openQ = 40; - bca->extQ = 20; - bca->tandemQ = 100; + bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; bca->min_baseQ = min_baseQ; bca->e = errmod_init(1. - theta); - return bca; + bca->min_frac = 0.002; + bca->min_support = 1; + 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); - free(bca->bases); free(bca); + if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; } + free(bca->bases); free(bca->inscns); free(bca); } - -int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r) +/* ref_base is the 4-bit representation of the reference base. It is + * negative if we are looking at an indel. */ +int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r) { - int i, n, ref4; + int i, n, ref4, is_indel, ori_depth = 0; memset(r, 0, sizeof(bcf_callret1_t)); - ref4 = bam_nt16_nt4_table[ref_base]; + if (ref_base >= 0) { + ref4 = bam_nt16_nt4_table[ref_base]; + is_indel = 0; + } else ref4 = 4, is_indel = 1; if (_n == 0) return -1; - // enlarge the bases array if necessary if (bca->max_bases < _n) { bca->max_bases = _n; @@ -48,24 +90,33 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf 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; + int q, b, mapQ, baseQ, is_diff, min_dist, seqQ; // set base if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; - baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality + ++ori_depth; + baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality + seqQ = is_indel? (p->aux>>8&0xff) : 99; if (q < bca->min_baseQ) continue; - mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ; + if (q > seqQ) q = seqQ; + 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; - b = bam1_seqi(bam1_seq(p->b), p->qpos); // base - b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base + if (!is_indel) { + b = bam1_seqi(bam1_seq(p->b), p->qpos); // base + b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base + is_diff = (ref4 < 4 && b == ref4)? 0 : 1; + } else { + 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; - is_diff = (ref4 < 4 && b == ref4)? 0 : 1; + 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; @@ -76,138 +127,177 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf 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->depth = n; r->ori_depth = ori_depth; // glfgen errmod_cal(bca->e, n, 5, bca->bases, r->p); return r->depth; } -int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r) +double mann_whitney_1947(int n, int m, int U) { - int i, n, n_ins, n_del; - memset(r, 0, sizeof(bcf_callret1_t)); - if (_n == 0) return -1; + 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); +} - // enlarge the bases array if necessary - if (bca->max_bases < _n) { - bca->max_bases = _n; - kroundup32(bca->max_bases); - bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); - } - // fill the bases array - memset(r, 0, sizeof(bcf_callret1_t)); - r->indelreg = 10000; - n_ins = n_del = 0; - for (i = n = 0; i < _n; ++i) { - const bam_pileup1_t *p = pl + i; - int q, b, mapQ, indelQ, is_diff, min_dist; - if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; - { // compute indel (base) quality - // this can be made more efficient, but realignment is the bottleneck anyway - int j, k, x, y, op, len = 0, max_left, max_rght, seqQ, indelreg; - bam1_core_t *c = &p->b->core; - uint32_t *cigar = bam1_cigar(p->b); - uint8_t *qual = bam1_qual(p->b); - for (k = y = 0, x = c->pos; k < c->n_cigar && y <= p->qpos; ++k) { - op = cigar[k]&0xf; - len = cigar[k]>>4; - if (op == BAM_CMATCH) { - if (pos > x && pos < x + len) break; - x += len; y += len; - } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += len; - else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += len; - } - if (k == c->n_cigar) continue; // this actually should not happen - max_left = max_rght = 0; indelreg = 0; - if (pos == x + len - 1 && k+2 < c->n_cigar && ((cigar[k+1]&0xf) == BAM_CINS || (cigar[k+1]&0xf) == BAM_CDEL) - && (cigar[k+2]&0xf) == BAM_CMATCH) - { - for (j = y; j < y + len; ++j) - if (max_left < qual[j]) max_left = qual[j]; - if ((cigar[k+1]&0xf) == BAM_CINS) y += cigar[k+1]>>4; - else x += cigar[k+1]>>4; - op = cigar[k+2]&0xf; len = cigar[k+2]>>4; - for (j = y; j < y + len; ++j) { - if (max_rght < qual[j]) max_rght = qual[j]; - if (qual[j] > BAM2BCF_INDELREG_THRES && indelreg == 0) - indelreg = j - y + 1; - } - if (r->indelreg > indelreg) r->indelreg = indelreg; - } else { - for (j = y; j <= p->qpos; ++j) - if (max_left < qual[j]) max_left = qual[j]; - for (j = p->qpos + 1; j < y + len; ++j) - if (max_rght < qual[j]) max_rght = qual[j]; - - } - indelQ = max_left < max_rght? max_left : max_rght; - // estimate the sequencing error rate - seqQ = bca->openQ; - if (p->indel != 0) seqQ += bca->extQ * (abs(p->indel) - 1); // FIXME: better to model homopolymer - if (p->indel > 0) { - ++n_ins; r->ins_len += p->indel; - } else if (p->indel < 0) { - ++n_del; r->del_len += -p->indel; - } - if (p->indel != 0) { // a different model for tandem repeats - uint8_t *seq = bam1_seq(p->b); - int tandemQ, qb = bam1_seqi(seq, p->qpos), l; - for (j = p->qpos + 1; j < c->l_qseq; ++j) - if (qb != bam1_seqi(seq, j)) break; - l = j; - for (j = (int)p->qpos - 1; j >= 0; --j) - if (qb != bam1_seqi(seq, j)) break; - l = l - (j + 1); - tandemQ = (int)((double)(abs(p->indel)) / l * bca->tandemQ + .499); - if (seqQ > tandemQ) seqQ = tandemQ; - } -// 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); - if (indelQ > seqQ) indelQ = seqQ; - q = indelQ; - } - if (q < bca->min_baseQ) continue; - mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ; - if (q > mapQ) q = mapQ; - if (q > 63) q = 63; - if (q < 4) q = 4; - b = p->indel? 1 : 0; - bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b; - // collect annotations - r->qsum[b] += q; - is_diff = b; - ++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; - if (min_dist > CAP_DIST) min_dist = CAP_DIST; - r->anno[1<<2|is_diff<<1|0] += indelQ; - r->anno[1<<2|is_diff<<1|1] += indelQ * indelQ; - r->anno[2<<2|is_diff<<1|0] += mapQ; - 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; - } - r->depth = n; - r->ins_len = n_ins? r->ins_len / n_ins : 0; - r->del_len = n_del? r->del_len / n_del : 0; - if (r->indelreg >= 10000) r->indelreg = 0; - // glfgen - errmod_cal(bca->e, n, 2, bca->bases, r->p); - return r->depth; +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); } -int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call) +/** + * 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; - call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base]; - call->ins_len = call->del_len = 0; call->indelreg = 0; - if (ref4 > 4) ref4 = 4; + if (ref_base >= 0) { + call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base]; + if (ref4 > 4) ref4 = 4; + } else call->ori_ref = -1, ref4 = 0; // calculate qsum memset(qsum, 0, 4 * sizeof(int)); 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 @@ -219,13 +309,24 @@ 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) + call->unseen = j, call->a[j++] = qsum[i]&3; + call->n_alleles = j; + } else { + call->n_alleles = j; + if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything } - if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0) - call->unseen = j, call->a[j++] = qsum[i]&3; - call->n_alleles = j; // set the PL array if (call->n < n) { call->n = n; @@ -237,8 +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; @@ -253,126 +354,100 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, PL[j] = y; } } +// if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen); call->shift = (int)(sum_min + .499); } // combine annotations memset(call->anno, 0, 16 * sizeof(int)); - for (i = call->depth = 0, tmp = 0; i < n; ++i) { + for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) { call->depth += calls[i].depth; + call->ori_depth += calls[i].ori_depth; for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j]; } - return 0; -} -int bcf_call_combine_gap(int n, const bcf_callret1_t *calls, bcf_call_t *call) -{ - int i, j, n_ins, n_del; - // combine annotations - call->ori_ref = 4; - memset(call->anno, 0, 16 * sizeof(int)); - call->ins_len = call->del_len = 0; call->indelreg = 10000; - for (i = call->depth = 0, n_ins = n_del = 0; i < n; ++i) { - const bcf_callret1_t *r = calls + i; - if (r->depth > 0) { - call->depth += r->depth; - if (r->ins_len > 0) { - call->ins_len += r->ins_len; - ++n_ins; - } - if (r->del_len > 0) { - call->del_len += r->del_len; - ++n_del; - } - if (r->indelreg > 0 && call->indelreg > r->indelreg) - call->indelreg = r->indelreg; - for (j = 0; j < 16; ++j) call->anno[j] += r->anno[j]; - } - } - if (call->depth == 0) return 0; // no indels - call->ins_len = n_ins? call->ins_len / n_ins : 0; - call->del_len = n_del? call->del_len / n_del : 0; - // - for (i = 0; i < 5; ++i) call->a[i] = -1; - call->a[0] = 0; call->a[1] = 1; - call->unseen = -1; - call->n_alleles = 2; - // set the PL array - if (call->n < n) { - call->n = n; - call->PL = realloc(call->PL, 15 * n); - } - { - int g[3]; - double sum_min = 0.; - g[0] = 0; g[1] = 1; g[2] = 3; - for (i = 0; i < n; ++i) { - uint8_t *PL = call->PL + 3 * i; - const bcf_callret1_t *r = calls + i; - float min = 1e37; - for (j = 0; j < 3; ++j) - if (min > r->p[g[j]]) min = r->p[g[j]]; - sum_min += min; - for (j = 0; j < 3; ++j) { - int y; - y = (int)(r->p[g[j]] - min + .499); - if (y > 255) y = 255; - PL[j] = y; - } - } - call->shift = (int)(sum_min + .499); - } + 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); kstring_t s; - int i; + int i, j; b->n_smpl = bc->n; b->tid = tid; b->pos = pos; b->qual = 0; s.s = b->str; s.m = b->m_str; s.l = 0; kputc('\0', &s); - if (bc->ins_len > 0 || bc->del_len > 0) { // an indel - for (i = 0; i < bc->indelreg; ++i) kputc('N', &s); + if (bc->ori_ref < 0) { // an indel + // write REF + kputc(ref[pos], &s); + for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s); kputc('\0', &s); - if (bc->ins_len > 0 && bc->del_len > 0) kputs("", &s); - else if (bc->ins_len > 0) kputs("", &s); - else if (bc->del_len > 0) kputs("", &s); - } else { // SNP + // write ALT + kputc(ref[pos], &s); + for (i = 1; i < 4; ++i) { + if (bc->a[i] < 0) break; + if (i > 1) { + kputc(',', &s); kputc(ref[pos], &s); + } + if (bca->indel_types[bc->a[i]] < 0) { // deletion + for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j) + kputc(ref[pos+1+j], &s); + } else { // insertion; cannot be a reference unless a bug + char *inscns = &bca->inscns[bc->a[i] * bca->maxins]; + for (j = 0; j < bca->indel_types[bc->a[i]]; ++j) + kputc("ACGTN"[(int)inscns[j]], &s); + for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s); + } + } + kputc('\0', &s); + } else { // a SNP kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s); for (i = 1; i < 5; ++i) { if (bc->a[i] < 0) break; if (i > 1) kputc(',', &s); kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s); } + kputc('\0', &s); } kputc('\0', &s); - kputc('\0', &s); // INFO - kputs("I16=", &s); + if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IS=%d,%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) {