X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_cat.c;h=a7502b9fd3784d6875862d69c14c1af00b86ae97;hb=0b3418cf166ce4a58cedf0d9a2df5ec3dd4cc5fa;hp=0fde045e1c6e319594c3453a6cdd6a1fac21e335;hpb=082f8688fa1360f8938e3ea353175b3ad471df81;p=samtools.git

diff --git a/bam_cat.c b/bam_cat.c
index 0fde045..a7502b9 100644
--- a/bam_cat.c
+++ b/bam_cat.c
@@ -59,6 +59,7 @@ all:bam_cat
 #include <stdlib.h>
 #include <unistd.h>
 
+#include "knetfile.h"
 #include "bgzf.h"
 #include "bam.h"
 
@@ -97,7 +98,7 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
             fprintf(stderr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);
             return -1;
         }
-        if (in->open_mode != 'r') return -1;
+        if (in->is_write) return -1;
         
         old = bam_header_read(in);
 		if (h == 0 && i == 0) bam_header_write(fp, old);
@@ -109,10 +110,10 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
         
         j=0;
 #ifdef _USE_KNETFILE
-        fp_file=fp->x.fpw;
-        while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) {
+        fp_file = fp->fp;
+        while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0) {
 #else  
-        fp_file=fp->file;
+        fp_file = fp->fp;
         while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {
 #endif
             if(len<es){