Patched the example makefile to not use samtools pileup, deprecated.

[samtools.git] / bgzf.h

diff --git a/bgzf.h b/bgzf.h
index 099ae9a6da1785ae132be55932a2e5c930ba49cc..7295f37425df320199aef87bb7bb80e482cc38bd 100644 (file)
--- a/bgzf.h
+++ b/bgzf.h
@@ -26,7 +26,6 @@
 
 #include <stdint.h>
 #include <stdio.h>
-#include <stdbool.h>
 #include <zlib.h>
 #ifdef _USE_KNETFILE
 #include "knetfile.h"
@@ -37,7 +36,7 @@
 typedef struct {
     int file_descriptor;
     char open_mode;  // 'r' or 'w'
-    bool owned_file, is_uncompressed;
+    int16_t owned_file, compress_level;
 #ifdef _USE_KNETFILE
        union {
                knetFile *fpr;
@@ -129,6 +128,7 @@ int bgzf_check_EOF(BGZF *fp);
 int bgzf_read_block(BGZF* fp);
 int bgzf_flush(BGZF* fp);
 int bgzf_flush_try(BGZF *fp, int size);
+int bgzf_check_bgzf(const char *fn);
 
 #ifdef __cplusplus
 }