Fix bgzip.exe and bcftools.exe handling large files and stdin/stdout

bcftools/index.c

@@ -206,7 +206,7 @@ static void download_from_remote(const char *url)
 
 static char *get_local_version(const char *fn)
 {
-    struct stat sbuf;
+    struct __stat64 sbuf;
     char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
     strcat(strcpy(fnidx, fn), ".bci");
     if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
@@ -215,15 +215,15 @@ static char *get_local_version(const char *fn)
         for (p = fnidx + l - 1; p >= fnidx; --p)
             if (*p == '/') break;
         url = fnidx; fnidx = strdup(p + 1);
-        if (stat(fnidx, &sbuf) == 0) {
+        if (_stat64(fnidx, &sbuf) == 0) {
             free(url);
             return fnidx;
         }
         fprintf(stderr, "[%s] downloading the index file...\n", __FUNCTION__);
         download_from_remote(url);
         free(url);
     }
-    if (stat(fnidx, &sbuf) == 0) return fnidx;
+    if (_stat64(fnidx, &sbuf) == 0) return fnidx;
     free(fnidx); return 0;
 }
 

bcftools/main.c

@@ -24,13 +24,13 @@ int bcf_cat(int n, char * const *fn)
         bcf_t *in;
         bcf_hdr_t *h;
         off_t end;
-        struct stat s;
+        struct __stat64 s;
         in = bcf_open(fn[i], "r");
         h = bcf_hdr_read(in);
         if (i == 0) bcf_hdr_write(out, h);
         bcf_hdr_destroy(h);
 #ifdef _USE_KNETFILE
-        fstat(knet_fileno(in->fp->x.fpr), &s);
+        _fstat64(knet_fileno(in->fp->x.fpr), &s);
         end = s.st_size - 28;
         while (knet_tell(in->fp->x.fpr) < end) {
             int size = knet_tell(in->fp->x.fpr) + BUF_SIZE < end? BUF_SIZE : end - knet_tell(in->fp->x.fpr);

bgzip.c

@@ -87,6 +87,9 @@ int main(int argc, char **argv)
     long start, end, size;
 
     _set_fmode(O_BINARY); //dong code, verify
+    _setmode(_fileno(stdout), O_BINARY);
+    _setmode(_fileno(stdin), O_BINARY);
+
     compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
     while((c  = getopt(argc, argv, "cdhfb:s:")) >= 0){
         switch(c){
@@ -104,13 +107,13 @@ int main(int argc, char **argv)
         return 1;
     }
     if (compress == 1) {
-        struct stat sbuf;
+        struct __stat64 sbuf;
         int f_src = _fileno(stdin);
         int f_dst = _fileno(stdout);
 
         if ( argc>optind )
         {
-            if ( stat(argv[optind],&sbuf)<0 ) 
+            if ( _stat64(argv[optind],&sbuf)<0 ) 
             { 
                 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
                 return 1; 
@@ -122,7 +125,7 @@ int main(int argc, char **argv)
             }
 
             if (pstdout)
-                f_dst = _fileno(stdout);
+                f_dst = _fileno(stdout); //redundant code, dong
             else
             {
                 char *name = malloc(strlen(argv[optind]) + 5);
@@ -147,14 +150,14 @@ int main(int argc, char **argv)
         _close(f_src);
         return 0;
     } else {
-        struct stat sbuf;
+        struct __stat64 sbuf;
         int f_dst;
 
         if ( argc>optind )
         {
             char *name;
             int len;
-            if ( stat(argv[optind],&sbuf)<0 )
+            if ( _stat64(argv[optind],&sbuf)<0 )
             {
                 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
                 return 1;