X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=53972de86f62bb717872d1cf6f4b651aac13ba4b;hb=998b354209b48256a4ffa6fa2be118ec7e021081;hp=a23477f40ec3147db38529140b09bac5531af54b;hpb=05cb7b5bb86b37e82a3ea7868b76031866303da2;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index a23477f..53972de 100644
--- 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");