X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=a383c45c1ea990cbb195f63e831e740011f7aa43;hb=d56f285da418ddbf9f3f33ab8ab247cfefc7b25c;hp=c6a571463cb608639dd23d71251ad2c70210c649;hpb=dec171ad7a34b3c819c166475dfbc95bce39c673;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index c6a5714..a383c45 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-31 (r448)"
+#define PACKAGE_VERSION "0.1.6-5 (r462)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -76,10 +76,8 @@ static int usage()
 	fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
 	fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
 	fprintf(stderr, "Usage:   samtools <command> [options]\n\n");
-	fprintf(stderr, "Command: import      import from SAM (obsolete; use `view')\n");
-	fprintf(stderr, "         view        export to the text format\n");
+	fprintf(stderr, "Command: view        SAM<->BAM conversion\n");
 	fprintf(stderr, "         sort        sort alignment file\n");
-	fprintf(stderr, "         merge       merge multiple sorted alignment files\n");
 	fprintf(stderr, "         pileup      generate pileup output\n");
 	fprintf(stderr, "         faidx       index/extract FASTA\n");
 #if _CURSES_LIB != 0
@@ -87,10 +85,11 @@ static int usage()
 #endif
 	fprintf(stderr, "         index       index alignment\n");
 	fprintf(stderr, "         fixmate     fix mate information\n");
-	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
 	fprintf(stderr, "         glfview     print GLFv3 file\n");
 	fprintf(stderr, "         flagstat    simple stats\n");
-	fprintf(stderr, "         fillmd      recalculate MD/NM tags and '=' bases\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, "\n");
 	return 1;
 }
@@ -118,6 +117,7 @@ int main(int argc, char *argv[])
 	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);
+	else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
 	else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
 #if _CURSES_LIB != 0
 	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);