Check fclose(stdout) at the end of main() [and miscellanea]

csq.c

@@ -149,6 +149,7 @@
 #include <errno.h>
 #include <unistd.h>
 #include <ctype.h>
+#include <strings.h>
 #include "bcftools.h"
 #include "filter.h"
 #include "regidx.h"

gff.c

@@ -29,6 +29,7 @@
 #include <assert.h>
 #include <inttypes.h>
 #include <string.h>
+#include <strings.h>
 #include <htslib/hts.h>
 #include <htslib/khash.h>
 #include <htslib/khash_str2int.h>

main.c

@@ -28,6 +28,7 @@ THE SOFTWARE.  */
 #include <unistd.h>
 #include <string.h>
 #include <ctype.h>
+#include <errno.h>
 #include <htslib/hts.h>
 #include "version.h"
 #include "bcftools.h"
@@ -300,7 +301,17 @@ int main(int argc, char *argv[])
     {
         if (cmds[i].func && strcmp(argv[1],cmds[i].alias)==0)
         {
-            return cmds[i].func(argc-1,argv+1);
+            int ret = cmds[i].func(argc-1,argv+1);
+
+            // For subcommands that may have produced substantial output on stdout,
+            // make a final check for delayed I/O errors. Ignore EBADF as other code
+            // may have already closed stdout.
+            if (fclose(stdout) != 0 && errno != EBADF) {
+                fprintf(stderr, "[E::%s] closing standard output failed\n", __func__);
+                return 1;
+            }
+
+            return ret;
         }
         i++;
     }

plugins/tag2tag.c

@@ -24,6 +24,7 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <strings.h>
 #include <getopt.h>
 #include <math.h>
 #include <inttypes.h>