- // 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 (!(conf->flag&MPLP_NO_INDEL)) {
+ // call MNPs
+ if (bcf_call_mnp_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref) >= 0) {
+ for (i = 0; i < gplp.n; ++i)
+ bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], B2B_REF_MNP, bca, bcr + i);
+ if (bcf_call_combine(gplp.n, bcr, B2B_REF_MNP, &bc) >= 0) {
+ b = calloc(1, sizeof(bcf1_t));
+ bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
+ (conf->flag&MPLP_FMT_SP), bca, ref);
+ bcf_write(bp, bh, b);
+ bcf_destroy(b);
+ bca->last_mnp_pos = pos;