-/*
- * 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
#include <stdint.h>
#include <stdio.h>
-#include "zlib.h"
#include <stdbool.h>
-//#include "zutil.h"
+#include <zlib.h>
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
//typedef int8_t bool;
typedef struct {
int file_descriptor;
char open_mode; // 'r' or 'w'
- bool owned_file;
+ 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;
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
* Return value is non-negative on success.
* Returns -1 on error.
*/
-int64_t bgzf_tell(BGZF* fp);
+#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
/*
* Set the file to read from the location specified by pos, which must
*/
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);
+int bgzf_read_block(BGZF* fp);
+int bgzf_flush(BGZF* fp);
+int bgzf_flush_try(BGZF *fp, int size);
+
#ifdef __cplusplus
}
#endif
+static inline int bgzf_getc(BGZF *fp)
+{
+ int c;
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) return -2; /* error */
+ if (fp->block_length == 0) return -1; /* end-of-file */
+ }
+ c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+ if (fp->block_offset == fp->block_length) {
+#ifdef _USE_KNETFILE
+ fp->block_address = knet_tell(fp->x.fpr);
+#else
+ fp->block_address = ftello(fp->file);
+#endif
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ return c;
+}
+
#endif