Updated samtools to 0.1.19

[rsem.git] / sam / bcftools / main.c

diff --git a/sam/bcftools/main.c b/sam/bcftools/main.c
index fcd94b821b8e46b483dc99d4feaf5487ccfc3d03..eda6217f75ecda8a901e8f66b2d34dee97c08b77 100644 (file)
--- a/sam/bcftools/main.c
+++ b/sam/bcftools/main.c
@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <sys/stat.h>
 #include <unistd.h>
+#include "knetfile.h"
 #include "bcf.h"
 
 #include "kseq.h"
@@ -29,12 +30,12 @@ int bcf_cat(int n, char * const *fn)
                if (i == 0) bcf_hdr_write(out, h);
                bcf_hdr_destroy(h);
 #ifdef _USE_KNETFILE
-               fstat(knet_fileno(in->fp->x.fpr), &s);
+               fstat(knet_fileno((knetFile*)in->fp->fp), &s);
                end = s.st_size - 28;
-               while (knet_tell(in->fp->x.fpr) < end) {
-                       int size = knet_tell(in->fp->x.fpr) + BUF_SIZE < end? BUF_SIZE : end - knet_tell(in->fp->x.fpr);
-                       knet_read(in->fp->x.fpr, buf, size);
-                       fwrite(buf, 1, size, out->fp->x.fpw);
+               while (knet_tell((knetFile*)in->fp->fp) < end) {
+                       int size = knet_tell((knetFile*)in->fp->fp) + BUF_SIZE < end? BUF_SIZE : end - knet_tell((knetFile*)in->fp->fp);
+                       knet_read(in->fp->fp, buf, size);
+                       fwrite(buf, 1, size, out->fp->fp);
                }
 #else
                abort(); // FIXME: not implemented