update to avoid test failure in windows

bgzip.c

@@ -41,6 +41,8 @@
 #ifdef _WIN32
 #  define WIN32_LEAN_AND_MEAN
 #  include <windows.h>
+#  include <io.h>                           //for _dup method
+#  undef _fileno                            //to use _fileno method instead of macro
 #endif
 
 static const int WINDOW_SIZE = BGZF_BLOCK_SIZE;
@@ -127,6 +129,37 @@ static int bgzip_main_usage(FILE *fp, int status)
     return status;
 }
 
+/// getstdinout - to get stdin/stdout duplicated, abtracting OS dependencies
+/** @param fd file descriptor to be duplicated
+ * returns duplicated descriptor on success -1 on failure
+ * the descriptor is set to BINARY mode in windows to avoid errors - both input as well as output
+ */
+int getstdinout(int fd)
+{
+    int dupfd = -1;
+#ifdef _WIN32
+    dupfd = _dup(fd);               //windows specific dup api
+    _setmode(dupfd, O_BINARY);      //set to binary mode
+#else
+    dupfd = dup(fd);
+#endif  //_WIN32
+
+    return dupfd;
+}
+
+/// getfileno - to get file descriptor from FILE pointer, abtracting OS dependencies
+/** @param fp FILE pointer
+ * returns file descriptor
+ */
+int getfileno(FILE *fp)
+{
+#ifdef _WIN32
+    return _fileno(fp);             //windows specific api
+#else
+    return fileno(fp);
+#endif  //_WIN32
+}
+
 int main(int argc, char **argv)
 {
     int c, compress, compress_level = -1, pstdout, is_forced, test, index = 0, rebgzip = 0, reindex = 0, keep, binary;
@@ -207,14 +240,14 @@ int main(int argc, char **argv)
                 out_mode_exclusive[2] = compress_level + '0';
             }
 
-            if (!(f_src = !isstdin ? hopen(argv[optind], "r") : hdopen(dup(STDIN_FILENO), "r"))) {
+            if (!(f_src = !isstdin ? hopen(argv[optind], "r") : hdopen(getstdinout(STDIN_FILENO), "r"))) {
                 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
                 return 1;
             }
             if ( argc>optind && !isstdin )
             {
                 if (pstdout)
-                    fp = bgzf_dopen(dup(STDOUT_FILENO), out_mode);
+                    fp = bgzf_dopen(getstdinout(STDOUT_FILENO), out_mode);
                 else
                 {
                     char *name = malloc(strlen(argv[optind]) + 5);
@@ -241,15 +274,15 @@ int main(int argc, char **argv)
                     free(name);
                 }
             }
-            else if (!pstdout && isatty(fileno((FILE *)stdout)) )
+            else if (!pstdout && isatty(getfileno((FILE *)stdout)) )
                 return bgzip_main_usage(stderr, EXIT_FAILURE);
             else if ( index && !index_fname )
             {
                 fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");
                 return 1;
             }
             else
-                fp = bgzf_dopen(dup(STDOUT_FILENO), out_mode);
+                fp = bgzf_dopen(getstdinout(STDOUT_FILENO), out_mode);
 
             if ( index && rebgzip )
             {
@@ -398,7 +431,7 @@ int main(int argc, char **argv)
             else
             {
                 if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n");
-                fp = bgzf_dopen(dup(STDIN_FILENO), "r");
+                fp = bgzf_dopen(getstdinout(STDIN_FILENO), "r");
                 if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno));
             }
 
@@ -441,7 +474,7 @@ int main(int argc, char **argv)
                 }
 
                 if (pstdout || test) {
-                    f_dst = dup(STDOUT_FILENO);
+                    f_dst = getstdinout(STDOUT_FILENO);
                 }
                 else {
                     const int wrflags = O_WRONLY | O_CREAT | O_TRUNC;
@@ -484,12 +517,12 @@ int main(int argc, char **argv)
                     free(name);
                 }
             }
-            else if (!pstdout && isatty(fileno((FILE *)stdin)))
+            else if (!pstdout && isatty(getfileno((FILE *)stdin)))
                 return bgzip_main_usage(stderr, EXIT_FAILURE);
             else
             {
-                f_dst = dup(STDOUT_FILENO);
-                fp = bgzf_dopen(dup(STDIN_FILENO), "r");
+                f_dst = getstdinout(STDOUT_FILENO);
+                fp = bgzf_dopen(getstdinout(STDIN_FILENO), "r");
                 if (fp == NULL) {
                     fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
                     return 1;