* samtools-0.1.7-9 (r586)

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index a383c45c1ea990cbb195f63e831e740011f7aa43..9edb6cb8402032cfa1cdbc7a97ce6b8c853914f1 100644 (file)
--- 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 "0.1.7-9 (r586)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -20,12 +20,12 @@ 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[]);
 
 int main_samview(int argc, char *argv[]);
 int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
 int glf3_view_main(int argc, char *argv[]);
@@ -88,8 +88,9 @@ 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, "         reheader    replace BAM header\n");
        fprintf(stderr, "\n");
        return 1;
 }
@@ -113,12 +114,12 @@ 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);
        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);
+       else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
 #if _CURSES_LIB != 0
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif