X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=902bd800454d1a338aa605f7e89ea916964eea78;hb=6ad0dc55ff3abf908a99935321ff8fa5efed4d88;hp=3742bb2454e0be3fc9005d9c4f6117103616ed92;hpb=521aa49c29217a0398ff5e186072df97cf9d80c4;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index 3742bb2..902bd80 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-34 (r451)"
+#define PACKAGE_VERSION "0.1.7-6 (r530)"
 #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[]);
 
@@ -78,7 +77,6 @@ static int usage()
 	fprintf(stderr, "Usage:   samtools <command> [options]\n\n");
 	fprintf(stderr, "Command: view        SAM<->BAM conversion\n");
 	fprintf(stderr, "         sort        sort alignment file\n");
-	fprintf(stderr, "         merge       merge sorted alignments (Picard recommended)\n");
 	fprintf(stderr, "         pileup      generate pileup output\n");
 	fprintf(stderr, "         faidx       index/extract FASTA\n");
 #if _CURSES_LIB != 0
@@ -86,10 +84,11 @@ static int usage()
 #endif
 	fprintf(stderr, "         index       index alignment\n");
 	fprintf(stderr, "         fixmate     fix mate information\n");
-	fprintf(stderr, "         rmdup       remove PCR duplicates (Picard recommended)\n");
 	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\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);