X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=a5a0da385224cdb79c20072dd2da3e5328f91af3;hb=6ed91e9cf6d11c718bc8b2bea412108555d55bba;hp=ebd1b9e2dc9aa55b8b3d45c9507861912d321274;hpb=4967051aa734ece6ce44f0fb891a936e849c2fe2;p=samtools.git

diff --git a/bamtk.c b/bamtk.c
index ebd1b9e..a5a0da3 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-15 (r592)"
+#define PACKAGE_VERSION "0.1.12-1 (r873)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -23,7 +23,7 @@ int bam_mating(int argc, char *argv[]);
 int bam_rmdup(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[]);
@@ -86,6 +86,7 @@ static int usage()
 	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, "         glfview     print GLFv3 file\n");
 	fprintf(stderr, "         flagstat    simple stats\n");
@@ -94,6 +95,12 @@ static int usage()
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
 	fprintf(stderr, "         reheader    replace BAM header\n");
 	fprintf(stderr, "\n");
+#ifdef _WIN32
+	fprintf(stderr, "\
+Note: The Windows version of SAMtools is mainly designed for read-only\n\
+      operations, such as viewing the alignments and generating the pileup.\n\
+      Binary files generated by the Windows version may be buggy.\n\n");
+#endif
 	return 1;
 }
 
@@ -114,6 +121,7 @@ int main(int argc, char *argv[])
 	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);