X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=20b1913efa09ce796392885b0f4b831c8c759f4a;hb=d195bcfb6632c68032a89c091c20dc24dd6ded60;hp=02d6c5bf7ea5b595709a5840bca387fef4d66add;hpb=d1643d6e5e6ec3a7cb1ef8b62b9a6f9b21ff2527;p=samtools.git

diff --git a/bam_md.c b/bam_md.c
index 02d6c5b..20b1913 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -315,7 +315,8 @@ int bam_fillmd(int argc, char *argv[])
 		fprintf(stderr, "         -b       compressed BAM output\n");
 		fprintf(stderr, "         -S       the input is SAM with header\n");
 		fprintf(stderr, "         -A       modify the quality string\n");
-		fprintf(stderr, "         -r       read-independent local realignment\n\n");
+		fprintf(stderr, "         -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
+		fprintf(stderr, "         -E       extended BAQ for better sensitivity but lower specificity\n\n");
 		return 1;
 	}
 	fp = samopen(argv[optind], mode_r, 0);