#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[]);
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->last_mnp_pos = -100;
bca->e = errmod_init(1. - theta);
return bca;
}
{
if (bca == 0) return;
errmod_destroy(bca->e);
- free(bca->bases); free(bca);
+ 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)
+/* Compute genotype likelihood by combining likelihood of each
+ * read. ref_base is the 4-bit representation of the reference base. It
+ * is negative if we are looking at an indel or an MNP. Indel and MNP
+ * are indistinguishable in this function. */
+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;
memset(r, 0, sizeof(bcf_callret1_t));
for (i = n = 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;
+ if (q > seqQ) q = seqQ;
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 = 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);
+ }
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;
++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[3<<2|is_diff<<1|0] += min_dist;
r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
}
- 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)
-{
- 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;
- 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;
- }
- } 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) { // 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;
- // glfgen
- errmod_cal(bca->e, n, 2, bca->bases, r->p);
- return r->depth;
-}
-
+/* Combine individual calls. ref_base is a 4-bit A/C/G/T for a SNP, or
+ * B2B_REF_MNP, or B2B_REF_INDEL. Indel and MNP are indistinguishable in
+ * this function. */
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];
- 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 = ref_base, ref4 = 0; // ref_base < 0
// calculate qsum
memset(qsum, 0, 4 * sizeof(int));
for (i = 0; i < n; ++i)
else break;
}
}
- if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
- call->unseen = j, call->a[j++] = qsum[i]&3;
- call->n_alleles = j;
+ 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 { // for indels and MNPs
+ call->n_alleles = j;
+ if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+ }
// set the PL array
if (call->n < n) {
call->n = n;
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_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
+/* Fill a bcf1_t record. The type of the record (SNP, MNP or INDEL) is
+ * determined by bca->ori_ref. */
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+ 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? 'X' : "ACGT"[bc->a[i]], &s);
+ if (bc->ori_ref == B2B_REF_INDEL) { // 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 if (bc->ori_ref == B2B_REF_MNP) {
+ for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+j], &s);
+ kputc('\0', &s);
+ for (i = 1; i < 4; ++i) {
+ if (bc->a[i] < 0) break;
+ if (i > 1) kputc(',', &s);
+ for (j = 0; j < bca->indelreg; ++j)
+ kputc("ACGT"[bca->indel_types[i]>>2*j&3], &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 == B2B_REF_INDEL) kputs("INDEL;", &s);
+ else if (bc->ori_ref == B2B_REF_MNP) kputs("MNP;", &s);
+ 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);