+void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
+{
+ bam_fillmd1_core(b, ref, is_equal, 0);
+}
+
+// local realignment
+
+#define MIN_REF_LEN 10
+
+int bam_realn(bam1_t *b, const char *ref)
+{
+ int k, l_ref, score, n_cigar;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *s_ref = 0, *s_read = 0, *seq;
+ ka_param_t par;
+ bam1_core_t *c = &b->core;
+ // set S/W parameters
+ par = ka_param_blast; par.gap_open = 4; par.gap_ext = 1; par.gap_end_open = par.gap_end_ext = 0;
+ // calculate the length of the reference in the alignment
+ for (k = l_ref = 0; k < c->n_cigar; ++k) {
+ if ((cigar[k]&0xf) == BAM_CREF_SKIP) break; // do not do realignment if there is an `N' operation
+ if ((cigar[k]&0xf) == BAM_CMATCH || (cigar[k]&0xf) == BAM_CDEL)
+ l_ref += cigar[k]>>4;
+ }
+ if (k != c->n_cigar || l_ref < MIN_REF_LEN) return -1;
+ for (k = 0; k < l_ref; ++k)
+ if (ref[c->pos + k] == 0) return -1; // the read stands out of the reference
+ // allocate
+ s_ref = calloc(l_ref, 1);
+ s_read = calloc(c->l_qseq, 1);
+ for (k = 0, seq = bam1_seq(b); k < c->l_qseq; ++k)
+ s_read[k] = bam_nt16_nt4_table[bam1_seqi(seq, k)];
+ for (k = 0; k < l_ref; ++k)
+ s_ref[k] = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[c->pos + k]]];
+ // do alignment
+ cigar = ka_global_core(s_ref, l_ref, s_read, c->l_qseq, &par, &score, &n_cigar);
+ if (score <= 0) { // realignment failed
+ free(cigar); free(s_ref); free(s_read);
+ return -1;
+ }
+ // copy over the alignment
+ if (4 * (n_cigar - (int)c->n_cigar) + b->data_len > b->m_data) { // enlarge b->data
+ b->m_data = 4 * (n_cigar - (int)c->n_cigar) + b->data_len;
+ kroundup32(b->m_data);
+ b->data = realloc(b->data, b->m_data);
+ }
+ if (n_cigar != (int)c->n_cigar) // move data
+ memmove(b->data + c->l_qname + 4 * n_cigar, bam1_seq(b), b->data_len - c->l_qseq - 4 * c->n_cigar);
+ memcpy(bam1_cigar(b), cigar, n_cigar * 4);
+ c->n_cigar = n_cigar;
+ free(s_ref); free(s_read); free(cigar);
+ return 0;
+}
+