added the phase command

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index 02d6c5bf7ea5b595709a5840bca387fef4d66add..20b1913efa09ce796392885b0f4b831c8c759f4a 100644 (file)
--- 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);