#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 CAP_DIST 25
-struct __bcf_callaux_t {
- int max_bases, capQ, min_baseQ;
- uint16_t *bases;
- errmod_t *e;
-};
-
bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
{
bcf_callaux_t *bca;
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->min_baseQ = min_baseQ;
bca->e = errmod_init(1. - theta);
return bca;
const bam_pileup1_t *p = pl + i;
int q, b, mapQ, baseQ, is_diff, min_dist;
// set base
- if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
+ 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
if (q < bca->min_baseQ) continue;
mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
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)
+{
+ int i, n, n_ins, n_del;
+ memset(r, 0, sizeof(bcf_callret1_t));
+ 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
+ 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;
+}
+
int bcf_call_combine(int n, const bcf_callret1_t *calls, 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;
// calculate qsum
memset(qsum, 0, 4 * sizeof(int));
return 0;
}
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
+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);
+ }
+ return 0;
+}
+
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
+{
+ extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
kstring_t s;
int i;
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? 'X' : "ACGT"[bc->a[i]], &s);
+ if (bc->ins_len > 0 || bc->del_len > 0) { // an indel
+ for (i = 0; i < bc->indelreg; ++i) kputc('N', &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
+ 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);
// FMT
- kputs("PL", &s); kputc('\0', &s);
+ kputs("PL", &s);
+ if (bcr) {
+ kputs(":DP", &s);
+ if (is_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;
+ 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 (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;
}
projects / samtools.git / blobdiff