bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0, (conf->flag&MPLP_FMT_SP));
bcf_write(bp, bh, b);
bcf_destroy(b);
+ // test if there is an indel
+ if (conf->flag&MPLP_REALN) {
+ for (i = 0; i < gplp.n; ++i) {
+ int j;
+ for (j = 0; j < gplp.n_plp[i]; ++j) {
+ const bam_pileup1_t *p = gplp.plp[i] + j;
+ if (p->indel != 0) break;
+ }
+ if (j != gplp.n_plp[i]) break;
+ }
+ if (i < gplp.n) { // at least one of the read contains a gap
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen_gap(pos, gplp.n_plp[i], gplp.plp[i], bca, bcr + i);
+ }
+ }
} else {
printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {