X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=d4b40eab0166dd062e04438dff8b69cedb5a9328;hb=d14782f26230244039bf38f6384a7a9106b0daed;hp=a7c67ab615024eddb843401730f1f393a132b19f;hpb=54f5a850f38a820669d614029b151080172eb953;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index a7c67ab..d4b40ea 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,23 +9,24 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-28 (r444)"
+#define PACKAGE_VERSION "0.1.8-12 (r693)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
 int bam_pileup(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
 int bam_merge(int argc, char *argv[]);
 int bam_index(int argc, char *argv[]);
 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 bam_idxstats(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[]);
@@ -76,21 +77,23 @@ 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, "         mpileup     multi-way pileup\n");
 	fprintf(stderr, "         faidx       index/extract FASTA\n");
 #if _CURSES_LIB != 0
 	fprintf(stderr, "         tview       text alignment viewer\n");
 #endif
 	fprintf(stderr, "         index       index alignment\n");
+	fprintf(stderr, "         idxstats    BAM index stats (r595 or later)\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\n");
+	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
+	fprintf(stderr, "         reheader    replace BAM header\n");
 	fprintf(stderr, "\n");
 	return 1;
 }
@@ -108,17 +111,20 @@ int main(int argc, char *argv[])
 	if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
 	else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
 	else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
+	else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
 	else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
 	else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
 	else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
+	else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
 	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