Avoid really closing stdin/stdout in hclose()/hts_close()/et al

hfile.c

@@ -524,7 +524,7 @@ void hclose_abruptly(hFILE *fp)
 typedef struct {
     hFILE base;
     int fd;
-    unsigned is_socket:1;
+    unsigned is_socket:1, is_shared:1;
 } hFILE_fd;
 
 static ssize_t fd_read(hFILE *fpv, void *buffer, size_t nbytes)
@@ -599,6 +599,10 @@ static int fd_close(hFILE *fpv)
 {
     hFILE_fd *fp = (hFILE_fd *) fpv;
     int ret;
+
+    // If we don't own the fd, return successfully without actually closing it
+    if (fp->is_shared) return 0;
+
     do {
 #ifdef HAVE_CLOSESOCKET
         ret = fp->is_socket? closesocket(fp->fd) : close(fp->fd);
@@ -636,6 +640,7 @@ static hFILE *hopen_fd(const char *filename, const char *mode)
 
     fp->fd = fd;
     fp->is_socket = 0;
+    fp->is_shared = 0;
     fp->base.backend = &fd_backend;
     return &fp->base;
 
@@ -702,6 +707,7 @@ hFILE *hdopen(int fd, const char *mode)
 
     fp->fd = fd;
     fp->is_socket = (strchr(mode, 's') != NULL);
+    fp->is_shared = (strchr(mode, 'S') != NULL);
     fp->base.backend = &fd_backend;
     return &fp->base;
 }
@@ -723,10 +729,12 @@ static hFILE *hopen_fd_fileuri(const char *url, const char *mode)
 static hFILE *hopen_fd_stdinout(const char *mode)
 {
     int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO;
+    char mode_shared[101];
+    snprintf(mode_shared, sizeof mode_shared, "S%s", mode);
 #if defined HAVE_SETMODE && defined O_BINARY
     if (setmode(fd, O_BINARY) < 0) return NULL;
 #endif
-    return hdopen(fd, mode);
+    return hdopen(fd, mode_shared);
 }
 
 HTSLIB_EXPORT

htsfile.c

@@ -31,7 +31,6 @@ DEALINGS IN THE SOFTWARE.  */
 #include <stdlib.h>
 #include <string.h>
 #include <getopt.h>
-#include <unistd.h>
 
 #include "htslib/hfile.h"
 #include "htslib/hts.h"
@@ -62,13 +61,6 @@ void error(const char *format, ...)
     status = EXIT_FAILURE;
 }
 
-static htsFile *dup_stdout(const char *mode)
-{
-    int fd = dup(STDOUT_FILENO);
-    hFILE *hfp = (fd >= 0)? hdopen(fd, mode) : NULL;
-    return hfp? hts_hopen(hfp, "-", mode) : NULL;
-}
-
 static void view_sam(samFile *in, const char *filename)
 {
     bam1_t *b = NULL;
@@ -81,7 +73,7 @@ static void view_sam(samFile *in, const char *filename)
         goto clean;
     }
 
-    out = dup_stdout("w");
+    out = hts_open("-", "w");
     if (out == NULL) { error("reopening standard output failed"); goto clean; }
 
     if (show_headers) {
@@ -125,7 +117,7 @@ static void view_vcf(vcfFile *in, const char *filename)
         goto clean;
     }
 
-    out = dup_stdout("w");
+    out = hts_open("-", "w");
     if (out == NULL) { error("reopening standard output failed"); goto clean; }
 
     if (show_headers) {
@@ -325,5 +317,8 @@ int main(int argc, char **argv)
         if (fp && hclose(fp) < 0) error("closing \"%s\" failed", argv[i]);
     }
 
+    if (fclose(stdout) != 0 && errno != EBADF)
+        error("closing standard output failed");
+
     return status;
 }

htslib/hfile.h

@@ -80,6 +80,10 @@ Note that the file must be opened in binary mode, or else
 there will be problems on platforms that make a difference
 between text and binary mode.
 
+By default, the returned hFILE "takes ownership" of the file descriptor
+and _fd_ will be closed by hclose(). When _mode_ contains `S` (shared fd),
+hclose() will destroy the hFILE but not close the underlying _fd_.
+
 For socket descriptors (on Windows), _mode_ should contain `s`.
 */
 HTSLIB_EXPORT

test/test_view.c

@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <config.h>
 
+#include <errno.h>
 #include <stdio.h>
 #include <unistd.h>
 #include <stdlib.h>
@@ -430,5 +431,10 @@ int main(int argc, char *argv[])
     if (p.pool)
         hts_tpool_destroy(p.pool);
 
+    if (fclose(stdout) != 0 && errno != EBADF) {
+        fprintf(stderr, "Error closing standard output.\n");
+        exit_code = EXIT_FAILURE;
+    }
+
     return exit_code;
 }