Fix error reporting after closing files

Calling bgzf_close() (and hts_close()) frees the file pointer, so the
errcode field cannot be accessed afterwards. Report errors as per errno
instead as is done in vcfconvert.c.

Also report the right file pointer's errcode after bgzf_write() failure.

Author: jmarshall

reheader.c

@@ -418,7 +418,7 @@ static void reheader_vcf_gz(args_t *args)
     // Output all remaining data read with the header block
     if ( fp->block_length - skip_until > 0 )
     {
-        if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode);
+        if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",bgzf_out->errcode);
     }
     if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode);
 
@@ -434,8 +434,8 @@ static void reheader_vcf_gz(args_t *args)
         int count = bgzf_raw_write(bgzf_out, buf, nread);
         if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
     }
-    if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %d\n",args->output_fname ? args->output_fname : "-",bgzf_out->errcode);
-    if (hts_close(args->fp)) error("Error closing %s: %d\n",args->fname,fp->errcode);
+    if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %s\n",args->output_fname ? args->output_fname : "-",strerror(errno));
+    if (hts_close(args->fp)) error("Error closing %s: %s\n",args->fname,strerror(errno));
     free(buf);
 }
 static void reheader_vcf(args_t *args)

vcfconcat.c

@@ -919,7 +919,7 @@ static void naive_concat(args_t *args)
         // Output all non-header data that were read together with the header block
         if ( fp->block_length - nskip > 0 )
         {
-            if ( bgzf_write(bgzf_out, (char *)fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("\nError: %d\n",fp->errcode);
+            if ( bgzf_write(bgzf_out, (char *)fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("\nError: %d\n",bgzf_out->errcode);
         }
         if ( bgzf_flush(bgzf_out)<0 ) error("\nError: %d\n",bgzf_out->errcode);
 
@@ -952,7 +952,7 @@ static void naive_concat(args_t *args)
     }
     free(buf);
     free(tmp.s);
-    if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
+    if (bgzf_close(bgzf_out) < 0) error("Error: %s\n",strerror(errno));
 }
 
 static void usage(args_t *args)