Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.

[samtools.git] / bam_reheader.c

diff --git a/bam_reheader.c b/bam_reheader.c
index bae97c796fc7a6116751ff809e9b9f28dc7d4063..661942841932ad005f8269cca81ab2db4e89aecf 100644 (file)
--- 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);