From b72959e1752f3d26cee0939ff9fb8789dd7d6af4 Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@hey.com>
Date: Mon, 27 Nov 2023 20:50:56 +1300
Subject: [PATCH 1/2] Check fclose(stdout) at the end of main() after running
 subcommands

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.
---
 main.c | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/main.c b/main.c
index a0213589f..f5618c56b 100644
--- a/main.c
+++ b/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++;
     }

From b56f39a7f1d7b6db92585cfbb3fff8c6883cb22e Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@hey.com>
Date: Mon, 27 Nov 2023 20:56:16 +1300
Subject: [PATCH 2/2] Include <strings.h> directly where needed [minor]

Other source files that use strcase*() functions #include <strings.h>
themselves, so do so for this source file too. (<strings.h> is often
a byproduct of <string.h> but POSIX doesn't require that.)
---
 csq.c             | 1 +
 gff.c             | 1 +
 plugins/tag2tag.c | 1 +
 3 files changed, 3 insertions(+)

diff --git a/csq.c b/csq.c
index f619e061a..5a11179a3 100644
--- a/csq.c
+++ b/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"
diff --git a/gff.c b/gff.c
index 5d9f062be..6ec5a5875 100644
--- a/gff.c
+++ b/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>
diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index 92ee2e478..387b9eec8 100644
--- a/plugins/tag2tag.c
+++ b/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>