#include <math.h>
#include <stdint.h>
+#include <assert.h>
#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 0.83f
+#define DEF_MAPQ 20
#define CAP_DIST 25
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; icig<p->b->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;
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;
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; i<bca->npos; 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; i<bca->npos; 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; i<bca->npos; i++)
+ {
+ if ( !bca->alt_pos[i] ) continue;
+ dp += bca->alt_pos[i];
+ int j = i<bca->npos/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; i<bca->npos; i++)
+ {
+ if ( !bca->alt_pos[i] ) continue;
+ int j = i<bca->npos/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
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;
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;
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("<INDEL>", &s);
- else if (bc->ins_len > 0) kputs("<INS>", &s);
- else if (bc->del_len > 0) kputs("<DEL>", &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;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)
{
projects / samtools.git / blobdiff