#include <stdlib.h>\r
#include <unistd.h>\r
\r
+#include "knetfile.h"\r
#include "bgzf.h"\r
#include "bam.h"\r
\r
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
\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