* samtools-0.1.12-6 (r887)

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index ebd1b9e2dc9aa55b8b3d45c9507861912d321274..9706069828948c274db15ffe99c2717c83ca9fe0 100644 (file)
--- 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 "0.1.12-6 (r887)"
 #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);