change the default correlation coefficient

[samtools.git] / bam_plcmd.c

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");