Added tests and changes to make the test work.

bgzip.c

@@ -297,9 +297,15 @@ int main(int argc, char **argv)
         return 1;
     }
 
-    if (write_fname && pstdout) {
-        fprintf(stderr, "[bgzip] Cannot write to %s and stdout at the same time.\n", write_fname);
-        return 1;
+    if (write_fname) {
+        if (pstdout) {
+            fprintf(stderr, "[bgzip] Cannot write to %s and stdout at the same time.\n", write_fname);
+            return 1;
+        } else if (strncmp(write_fname, "-", strlen(write_fname)) == 0) {
+            // stdout has special handling so treat as -c
+            pstdout = 1;
+            write_fname = NULL;
+        }
     }
 
     do {
@@ -713,16 +719,19 @@ int main(int argc, char **argv)
             if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode);
 
             if (statfilename) {
-                //get input file timestamp
-                if (!getfilespec(argv[optind], &filestat)) {
-                    //set output file timestamp
-                    if (setfilespec(statfilename, &filestat) < 0) {
-                        fprintf(stderr, "[bgzip] Failed to set file specification.\n");
+                if (!write_fname) {
+                    //get input file timestamp
+                    if (!getfilespec(argv[optind], &filestat)) {
+                        //set output file timestamp
+                        if (setfilespec(statfilename, &filestat) < 0) {
+                            fprintf(stderr, "[bgzip] Failed to set file specification.\n");
+                        }
+                    }
+                    else {
+                        fprintf(stderr, "[bgzip] Failed to get file specification.\n");
                     }
                 }
-                else {
-                    fprintf(stderr, "[bgzip] Failed to get file specification.\n");
-                }
+
                 free(statfilename);
             }
 

test/test.pl

@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 #
-#    Copyright (C) 2012-2023 Genome Research Ltd.
+#    Copyright (C) 2012-2024 Genome Research Ltd.
 #
 #    Author: Petr Danecek <pd3@sanger.ac.uk>
 #
@@ -589,6 +589,36 @@ sub test_bgzip {
         return;
     }
     passed($opts,$test);
+
+    # try writing to an explicit file name, round trip test
+    $test = sprintf('%s %2s threads', 'bgzip --output',
+                    $threads ? $threads : 'no');
+    print "$test: ";
+
+    my $compressed_op = "$$opts{tmp}/arbitrary.$threads.gz";
+    my $uncompressed_op = "$$opts{tmp}/arbitrary.$threads.txt";
+
+    $c = "$$opts{bin}/bgzip $at '$data' -o '$compressed_op'";
+
+    ($ret, $out) = _cmd($c);
+    if ($ret) {
+        failed($opts, $test, "non-zero exit from $c");
+        return;
+    }
+    $c = "$$opts{bin}/bgzip $at -d $compressed_op --output '$uncompressed_op'";
+
+    ($ret, $out) = _cmd($c);
+    if ($ret) {
+        failed($opts, $test, "non-zero exit from $c");
+        return;
+    }
+    $c = "cmp '$data' '$uncompressed_op'";
+    ($ret, $out) = _cmd($c);
+    if ($ret) {
+        failed($opts, $test, $out ? $out : "'$data' '$uncompressed_op' differ");
+        return;
+    }
+    passed($opts,$test);
 }
 
 my $test_view_failures;