bm = (bam_maqcns_t*)calloc(1, sizeof(bam_maqcns_t));
bm->aux = (bmc_aux_t*)calloc(1, sizeof(bmc_aux_t));
bm->het_rate = 0.001;
- bm->theta = 0.85;
+ bm->theta = 0.83f;
bm->n_hap = 2;
bm->eta = 0.03;
bm->cap_mapQ = 60;
for (i = 0; i < n_types; ++i) {
ka_param_t ap = ka_param_blast;
ap.band_width = 2 * types[n_types - 1] + 2;
- ap.gap_end = 0;
+ ap.gap_end_ext = 0;
// write ref2
for (k = 0, j = left; j <= pos; ++j)
ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];