bca->capQ = 60;
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;
}
errmod_destroy(bca->e);
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. */
+/* 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, is_indel;
+ 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];
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;
+ ++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;
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>>8&0x3f;
+ b = p->aux>>16&0x3f;
is_diff = (b != 0);
}
bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
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;
}
-
+/* 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];
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;
+ } 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)
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;
+ } 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;
}
// 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;
}
-
+/* 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)
{
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->ori_ref < 0) { // an indel
+ 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);
+ } 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) {
}
kputc('\0', &s);
// INFO
- if (bc->ori_ref < 0) kputs("INDEL;", &s);
- 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);