*

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index fb000a6425f3ea7246d6273e73d0f74cb6701166..ef0e052113b8ab7331cc084f4cc30bce6c59ce69 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -1,10 +1,15 @@
 #include <stdio.h>
 #include <unistd.h>
 #include <assert.h>
+#include <fcntl.h>
 #include "bam.h"
 
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-9 (r405)"
+#define PACKAGE_VERSION "0.1.5-29 (r445)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -85,13 +90,20 @@ static int usage()
        fprintf(stderr, "         rmdup       remove PCR duplicates\n");
        fprintf(stderr, "         glfview     print GLFv3 file\n");
        fprintf(stderr, "         flagstat    simple stats\n");
-       fprintf(stderr, "         fillmd      fill the MD tag and change identical base to =\n");
+       fprintf(stderr, "         fillmd      recalculate MD/NM tags and '=' bases\n");
        fprintf(stderr, "\n");
        return 1;
 }
 
 int main(int argc, char *argv[])
 {
+#ifdef _WIN32
+       setmode(fileno(stdout), O_BINARY);
+       setmode(fileno(stdin),  O_BINARY);
+#ifdef _USE_KNETFILE
+       knet_win32_init();
+#endif
+#endif
        if (argc < 2) return usage();
        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);