return max_i - pos;
}
+/*
+ * @n: number of samples
+ */
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash)
{
// To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
// check the number of N's in the sequence and skip places where half or more reference bases are Ns.
int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
- if ( nN*2>i ) { free(aux); return -1; }
+ if ( nN*2>(i-pos) ) { free(aux); return -1; }
ks_introsort(uint32_t, m, aux);
// squeeze out identical types
* reduces the power because sometimes, substitutions caused by
* indels are not distinguishable from true mutations. Multiple
* sequence realignment helps to increase the power.
+ *
+ * Masks mismatches present in at least 70% of the reads with 'N'.
*/
{ // construct per-sample consensus
int L = right - left + 1, max_i, max2_i;
if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
if (max_i >= 0) r[max_i] = 15;
if (max2_i >= 0) r[max2_i] = 15;
-// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
+ //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
}
free(ref0); free(cns);
}
}
}
// construct the consensus sequence
- max_ins = types[n_types - 1]; // max_ins is at least 0
+ max_ins = types[n_types - 1]; // max_ins is at least 0
if (max_ins > 0) {
- int *inscns_aux = calloc(4 * n_types * max_ins, sizeof(int));
+ int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
// count the number of occurrences of each base at each position for each type of insertion
for (t = 0; t < n_types; ++t) {
if (types[t] > 0) {
uint8_t *seq = bam1_seq(p->b);
for (k = 1; k <= p->indel; ++k) {
int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
- if (c < 4) ++inscns_aux[(t*max_ins+(k-1))*4 + c];
+ assert(c<5);
+ ++inscns_aux[(t*max_ins+(k-1))*5 + c];
}
}
}
inscns = calloc(n_types * max_ins, 1);
for (t = 0; t < n_types; ++t) {
for (j = 0; j < types[t]; ++j) {
- int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*4];
- for (k = 0; k < 4; ++k)
+ int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+ for (k = 0; k < 5; ++k)
if (ia[k] > max)
max = ia[k], max_k = k;
inscns[t*max_ins + j] = max? max_k : 4;
+ if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's
}
}
free(inscns_aux);