X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=bdd8578cb68b1c9c76ec4caa07c388478c78971d;hb=87d9ea7a580d0d1a58b8f0dca3ba3528ca118e46;hp=a383c45c1ea990cbb195f63e831e740011f7aa43;hpb=d56f285da418ddbf9f3f33ab8ab247cfefc7b25c;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index a383c45..bdd8578 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6-5 (r462)"
+#define PACKAGE_VERSION "0.1.6-18 (r493)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -20,7 +20,6 @@ int bam_sort(int argc, char *argv[]);
 int bam_tview_main(int argc, char *argv[]);
 int bam_mating(int argc, char *argv[]);
 int bam_rmdup(int argc, char *argv[]);
-int bam_rmdupse(int argc, char *argv[]);
 int bam_flagstat(int argc, char *argv[]);
 int bam_fillmd(int argc, char *argv[]);
 
@@ -88,8 +87,8 @@ static int usage()
 	fprintf(stderr, "         glfview     print GLFv3 file\n");
 	fprintf(stderr, "         flagstat    simple stats\n");
 	fprintf(stderr, "         calmd       recalculate MD/NM tags and '=' bases\n");
-	fprintf(stderr, "         merge       merge sorted alignments (Picard recommended)\n");
-	fprintf(stderr, "         rmdup       remove PCR duplicates (Picard recommended)\n");
+	fprintf(stderr, "         merge       merge sorted alignments\n");
+	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
 	fprintf(stderr, "\n");
 	return 1;
 }
@@ -113,7 +112,6 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
 	else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
 	else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
-	else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(argc-1, argv+1);
 	else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
 	else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
 	else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);