Check fclose(stdout) at the end of main()

Since PR samtools/htslib#1665, hts_open("-", "w") / hts_close() no longer
actually closes stdout. Close it at the end of main() so there is an
opportunity to detect I/O errors in previously-uncommitted writes.

Ignore EBADF as other code may have already closed stdout, e.g., either
particular subcommands or when (dynamically) linked against an older
version of HTSlib.

bamtk.c

@@ -303,5 +303,14 @@ int main(int argc, char *argv[])
         fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
         return 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) {
+        print_error_errno(argv[1], "closing standard output failed");
+        return 1;
+    }
+
     return ret;
 }