* samtools-0.1.6-18 (r493)

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 3742bb2454e0be3fc9005d9c4f6117103616ed92..bdd8578cb68b1c9c76ec4caa07c388478c78971d 100644 (file)
--- 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 "0.1.6-18 (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[]);
 
@@ -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);