modified: src/bam_pick.c

	modified:   src/usage.c

src/bam_pick.c

@@ -57,8 +57,7 @@ static int parse_args(int argc, char **argv)
         const char **var = 0;
         if (strcmp(a, "-list") == 0) var = &extract_fname;
         else if (strcmp(a, "-o") == 0) var = &args.output_fname;
-        else if (strcmp(a, "-tags") == 0) var = &tag_str;
-        else if (strcmp(a, "-tag") == 0) error("Did you mean -tags ?");
+        else if (strcmp(a, "-tags") == 0 || strcmp(a, "-tag") == 0) var = &tag_str;
         else if (strcmp(a, "-h") == 0 || strcmp(a, "--help") == 0) return 1;
         else if (strcmp(a, "-@") == 0) var = &file_th;
         else if (strcmp(a, "-q") == 0) var = &mapq;

src/usage.c

@@ -281,6 +281,7 @@ int anno_usage()
     fprintf(stderr, "                       Also generate junction name (chr:exon1_end-exon2_start/[+-]/Gene) in JC tag.\n");
     fprintf(stderr, " -flatten              Split overlapped exons into nonoverlapped bins.\n");
     fprintf(stderr, " -psi                  Annotate exclude reads tag (ER) for each exon.\n");
+    fprintf(stderr, " -vague-edge [INT]     Junction reads not exactly spliced at splice site and gene ends are allowed. Used to annotate third generation reads.\n");
     fprintf(stderr, "\n");
     //fprintf(stderr, " -as                   Annotate antisense RNAs. **experiment**\n");
     fprintf(stderr, " -tss                  Annotate reads start from TSS, designed for capped library. **experiment**\n");