X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_reheader.c;h=661942841932ad005f8269cca81ab2db4e89aecf;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=bae97c796fc7a6116751ff809e9b9f28dc7d4063;hpb=de48a5efc453a2fba80a1236b6bab37ecfd85260;p=samtools.git

diff --git a/bam_reheader.c b/bam_reheader.c
index bae97c7..6619428 100644
--- a/bam_reheader.c
+++ b/bam_reheader.c
@@ -1,5 +1,6 @@
 #include <stdio.h>
 #include <stdlib.h>
+#include "knetfile.h"
 #include "bgzf.h"
 #include "bam.h"
 
@@ -11,7 +12,7 @@ int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
 	bam_header_t *old;
 	int len;
 	uint8_t *buf;
-	if (in->open_mode != 'r') return -1;
+	if (in->is_write) return -1;
 	buf = malloc(BUF_SIZE);
 	old = bam_header_read(in);
 	fp = bgzf_fdopen(fd, "w");
@@ -21,11 +22,12 @@ int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
 		bgzf_flush(fp);
 	}
 #ifdef _USE_KNETFILE
-	while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+	while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0)
+		fwrite(buf, 1, len, fp->fp);
 #else
 	while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+		fwrite(buf, 1, len, fp->file);
 #endif
-		fwrite(buf, 1, len, fp->x.fpw);
 	free(buf);
 	fp->block_offset = in->block_offset = 0;
 	bgzf_close(fp);