A bug fix, "samtools view" is now working again.

[samtools.git] / bgzf.h

diff --git a/bgzf.h b/bgzf.h
index ca5e7ab08b53723491b18534a48e03b7188fbba7..91b33177ff07c667b16f4db2ab724081beee5499 100644 (file)
--- a/bgzf.h
+++ b/bgzf.h
@@ -1,13 +1,25 @@
-/*
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2008 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever.
- * Neither the Broad Institute nor MIT can be responsible for its use, misuse,
- * or functionality.
- */
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
 
 #ifndef __BGZF_H
 #define __BGZF_H
@@ -16,6 +28,9 @@
 #include <stdio.h>
 #include <stdbool.h>
 #include <zlib.h>
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
 
 //typedef int8_t bool;
 
@@ -23,7 +38,14 @@ typedef struct {
     int file_descriptor;
     char open_mode;  // 'r' or 'w'
     bool owned_file, is_uncompressed;
+#ifdef _USE_KNETFILE
+       union {
+               knetFile *fpr;
+               FILE *fpw;
+       } x;
+#else
     FILE* file;
+#endif
     int uncompressed_block_size;
     int compressed_block_size;
     void* uncompressed_block;
@@ -31,7 +53,9 @@ typedef struct {
     int64_t block_address;
     int block_length;
     int block_offset;
+       int cache_size;
     const char* error;
+       void *cache; // a pointer to a hash table
 } BGZF;
 
 #ifdef __cplusplus
@@ -94,6 +118,15 @@ int64_t bgzf_tell(BGZF* fp);
  */
 int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
 
+/*
+ * Set the cache size. Zero to disable. By default, caching is
+ * disabled. The recommended cache size for frequent random access is
+ * about 8M bytes.
+ */
+void bgzf_set_cache_size(BGZF *fp, int cache_size);
+
+int bgzf_check_EOF(BGZF *fp);
+
 #ifdef __cplusplus
 }
 #endif