change the default correlation coefficient

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 9caa5d7b4dfac43d166d163339547a82def69ca3..dfc83e9407e3bf635be009af4d4be50240c13e61 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -110,7 +110,7 @@ bam_maqcns_t *bam_maqcns_init()
        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;

diff --git a/bam_plcmd.c b/bam_plcmd.c
index a23477f40ec3147db38529140b09bac5531af54b..53972de86f62bb717872d1cf6f4b651aac13ba4b 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -375,6 +375,8 @@ int bam_pileup(int argc, char *argv[])
                default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
                }
        }
+       if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02;
+       if (d->c->theta > 1.0) d->c->theta = 1.0;
        if (fn_list) is_SAM = 1;
        if (optind == argc) {
                fprintf(stderr, "\n");