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);
}
-/* 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. */
+/* 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;
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 = ref_base, ref4 = 0; // ref_base < 0
+ } else call->ori_ref = -1, ref4 = 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 { // for indels and MNPs
+ } else {
call->n_alleles = j;
if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
}
}
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 == B2B_REF_INDEL) { // an indel
+ 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);
- } 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*i&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 == B2B_REF_INDEL) kputs("INDEL;", &s);
- else if (bc->ori_ref == B2B_REF_MNP) kputs("MNP;", &s);
+ if (bc->ori_ref < 0) kputs("INDEL;", &s);
kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
for (i = 0; i < 16; ++i) {
if (i) kputc(',', &s);