X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=340b10b8ff2ebfc1807af7f2c3b30b35a3dade3e;hb=fdec84077cb242e672bd3a62292c236edeb6236a;hp=d69c771da80ef14ed925e549548f988a766ae680;hpb=6f1c7227019c299bd9df4c4187ca29e0baad1c4b;p=samtools.git diff --git a/bam2bcf.c b/bam2bcf.c index d69c771..340b10b 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -1,186 +1,332 @@ #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[]); #define CALL_ETA 0.03f #define CALL_MAX 256 -#define CALL_DEFTHETA 0.85f +#define CALL_DEFTHETA 0.83f +#define DEF_MAPQ 20 -struct __bcf_callaux_t { - int max_info, capQ; - double *fk; - uint32_t *info; -}; +#define CAP_DIST 25 -bcf_callaux_t *bcf_call_init(double theta) +bcf_callaux_t *bcf_call_init(double theta, int min_baseQ) { bcf_callaux_t *bca; - int n; if (theta <= 0.) theta = CALL_DEFTHETA; bca = calloc(1, sizeof(bcf_callaux_t)); bca->capQ = 60; - bca->fk = calloc(CALL_MAX, sizeof(double)); - bca->fk[0] = 1.; - for (n = 1; n < CALL_MAX; ++n) - bca->fk[n] = theta >= 1.? 1. : pow(theta, n) * (1.0 - CALL_ETA) + CALL_ETA; - bca->fk[CALL_MAX-1] = 0.; - return bca; + bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; + bca->min_baseQ = min_baseQ; + bca->e = errmod_init(1. - theta); + 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; } -void bcf_call_destroy(bcf_callaux_t *bca) + +static int get_position(const bam_pileup1_t *p, int *len) { - if (bca) { - free(bca->info); free(bca->fk); free(bca); - } + 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; } -typedef struct { - float esum[5], fsum[5]; - uint32_t c[5]; - int w[8]; -} auxaux_t; - -/* - The following code is nearly identical to bam_maqcns_glfgen() under - the simplified SOAPsnp model. It does the following: - - 1) Collect strand, base, quality and mapping quality information for - each base and combine them in an integer: - - x = min{baseQ,mapQ}<<24 | 1<<21 | strand<<18 | base<<16 | baseQ<<8 | mapQ +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 + * 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, is_indel, ori_depth = 0; + memset(r, 0, sizeof(bcf_callret1_t)); + 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; + kroundup32(bca->max_bases); + bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); + } + // fill the bases array + 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 + if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; + ++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; + 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; + 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 + 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; + if (min_dist > CAP_DIST) min_dist = CAP_DIST; + r->anno[1<<2|is_diff<<1|0] += baseQ; + r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ; + 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; - 2) Sort the list of integers for the next step. + // 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 + errmod_cal(bca->e, n, 5, bca->bases, r->p); + return r->depth; +} - 3) For each base, calculate e_b, the sum of weighted qualities. For - each type of base on each strand, the best quality has the highest - weight. Only the top 255 bases on each strand are used (different - from maqcns). +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); +} - 4) Rescale the total read depth to 255. +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; + } - 5) Calculate Q(D|g) = -10\log_{10}P(D|g) (d_a is the allele count): + 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); + } +} - Q(D|)=\sum_{b\not=a}e_b - Q(D|)=3*(d_a+d_A)+\sum_{b\not=a,b\not=A}e_b - */ -int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r) +float mean_diff_to_prob(float mdiff, int dp, int readlen) { - int i, j, k, c, n; - float *p = r->p; - auxaux_t aux; + 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); + } - memset(r, 0, sizeof(bcf_callret1_t)); - if (_n == 0) return -1; + // 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} }; - // enlarge the aux array if necessary - if (bca->max_info < _n) { - bca->max_info = _n; - kroundup32(bca->max_info); - bca->info = (uint32_t*)realloc(bca->info, 4 * bca->max_info); - } - // fill the aux array - for (i = n = 0; i < _n; ++i) { - const bam_pileup1_t *p = pl + i; - uint32_t q, x = 0, qq; - if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases - q = (uint32_t)bam1_qual(p->b)[p->qpos]; // base quality - x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual; - if (p->b->core.qual < q) q = p->b->core.qual; // cap the overall quality at mapping quality - x |= q << 24; - qq = bam1_seqi(bam1_seq(p->b), p->qpos); // base - q = bam_nt16_nt4_table[qq? qq : ref_base]; // q is the 2-bit base - if (q < 4) x |= 1 << 21 | q << 16; - - bca->info[n++] = x; - } - ks_introsort_uint32_t(n, bca->info); - r->depth = n; - // generate esum and fsum - memset(&aux, 0, sizeof(auxaux_t)); - for (j = n - 1, r->sum_Q2 = 0; j >= 0; --j) { // calculate esum and fsum - uint32_t info = bca->info[j]; - int tmp; - if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | (info&0xffffff); - k = info>>16&7; - if (info>>24 > 0) { - aux.esum[k&3] += bca->fk[aux.w[k]] * (info>>24); - aux.fsum[k&3] += bca->fk[aux.w[k]]; - if (aux.w[k] + 1 < CALL_MAX) ++aux.w[k]; - ++aux.c[k&3]; - } - tmp = (int)(info&0xff) < bca->capQ? (int)(info&0xff) : bca->capQ; - r->sum_Q2 += tmp * tmp; - } - memcpy(r->esum, aux.esum, 5 * sizeof(float)); - // rescale ->c[] - for (j = c = 0; j != 4; ++j) c += aux.c[j]; - if (c > 255) { - for (j = 0; j != 4; ++j) aux.c[j] = (int)(254.0 * aux.c[j] / c + 0.499); - for (j = c = 0; j != 4; ++j) c += aux.c[j]; - } - // generate likelihood - for (j = 0; j != 5; ++j) { - float tmp; - // homozygous - for (k = 0, tmp = 0.0; k != 5; ++k) - if (j != k) tmp += aux.esum[k]; - p[j*5+j] = tmp; // anything that is not j - // heterozygous - for (k = j + 1; k < 5; ++k) { - for (i = 0, tmp = 0.0; i != 5; ++i) - if (i != j && i != k) tmp += aux.esum[i]; - p[j*5+k] = p[k*5+j] = 3.01 * (aux.c[j] + aux.c[k]) + tmp; - } - } - return 0; + 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)); } -/* - 1) Find the top 2 bases (from esum[4]). +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); +} - 2) If the reference base is among the top 2, consider the locus is - potentially biallelic and set call->a[2] as -1; otherwise, the - locus is potentially triallelic. If the reference is ambiguous, - take the weakest call as the pseudo-reference. +/** + * 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, int ref_base /*4-bit*/, bcf_call_t *call) +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; - int64_t sum[5], tmp; - call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base]; - if (ref4 > 4) ref4 = 4; - { // calculate esum - double esum[5]; - memset(esum, 0, sizeof(double) * 4); - for (i = 0; i < n; ++i) { - for (j = 0; j < 4; ++j) - esum[j] += calls[i].esum[j]; - } + int ref4, i, j, qsum[4]; + int64_t tmp; + 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) - sum[j] = (int)(esum[j] * 100. + .499) << 2 | 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 - for (j = i; j > 0 && sum[j] < sum[j-1]; --j) - tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp; + for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j) + tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp; // set the reference allele and alternative allele(s) for (i = 0; i < 5; ++i) call->a[i] = -1; call->unseen = -1; call->a[0] = ref4; for (i = 3, j = 1; i >= 0; --i) { - if ((sum[i]&3) != ref4) { - if (sum[i]>>2 != 0) call->a[j++] = sum[i]&3; + if ((qsum[i]&3) != ref4) { + 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++] = sum[i]&3; - call->n_alleles = j; // set the PL array if (call->n < n) { call->n = n; @@ -192,8 +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; @@ -208,36 +354,114 @@ 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); } - for (i = call->depth = 0, tmp = 0; i < n; ++i) { + // combine annotations + memset(call->anno, 0, 16 * sizeof(int)); + for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) { call->depth += calls[i].depth; - tmp += calls[i].sum_Q2; + call->ori_depth += calls[i].ori_depth; + for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j]; } - call->rmsQ = (int)(sqrt((double)tmp / call->depth) + .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) +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); - 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 && i != 3? 'X' : "ACGT"[bc->a[i]], &s); - kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &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); + // 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); + // INFO + 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 && 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); - kputs("MQ=", &s); kputw(bc->rmsQ, &s); kputs(";DP=", &s); kputw(bc->depth, &s); kputc('\0', &s); - kputs("PL", &s); kputc('\0', &s); b->m_str = s.m; b->str = s.s; b->l_str = s.l; - bcf_sync(bc->n, b); + bcf_sync(b); memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n); + 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; + 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) + { + sp[i] = 0; + } else { + double left, right, two; + int x; + kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two); + x = (int)(-4.343 * log(two) + .499); + if (x > 255) x = 255; + sp[i] = x; + } + } + } + } return 0; }