Updated samtools to 0.1.19

[rsem.git] / sam / bam_cat.c

diff --git a/sam/bam_cat.c b/sam/bam_cat.c
index 0fde045e1c6e319594c3453a6cdd6a1fac21e335..a7502b9fd3784d6875862d69c14c1af00b86ae97 100644 (file)
--- a/sam/bam_cat.c
+++ b/sam/bam_cat.c
@@ -59,6 +59,7 @@ all:bam_cat
 #include <stdlib.h>\r
 #include <unistd.h>\r
 \r
+#include "knetfile.h"\r
 #include "bgzf.h"\r
 #include "bam.h"\r
 \r
@@ -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]);\r
             return -1;\r
         }\r
-        if (in->open_mode != 'r') return -1;\r
+        if (in->is_write) return -1;\r
         \r
         old = bam_header_read(in);\r
                if (h == 0 && i == 0) bam_header_write(fp, old);\r
@@ -109,10 +110,10 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
         \r
         j=0;\r
 #ifdef _USE_KNETFILE\r
-        fp_file=fp->x.fpw;\r
-        while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) {\r
+        fp_file = fp->fp;\r
+        while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0) {\r
 #else  \r
-        fp_file=fp->file;\r
+        fp_file = fp->fp;\r
         while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {\r
 #endif\r
             if(len<es){\r