Thanks to visit codestin.com
Credit goes to code.bioconductor.org

src/razf.h
c1100b9b
  /*-
  * RAZF : Random Access compressed(Z) File
  * Version: 1.0
  * Release Date: 2008-10-27
  *
  * Copyright 2008, Jue Ruan <[email protected]>, Heng Li <[email protected]>
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions
  * are met:
  * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the distribution.
  *
  * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
  * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
  * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
  * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
  * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
  * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  */
 
 
 #ifndef __RAZF_RJ_H
 #define __RAZF_RJ_H
 
 #include <stdint.h>
 #include <stdio.h>
 #include "zlib.h"
 
 #ifdef _USE_KNETFILE
 #include "knetfile.h"
 #endif
 
 #if ZLIB_VERNUM < 0x1221
 #define _RZ_READONLY
 struct _gz_header_s;
 typedef struct _gz_header_s _gz_header;
 #define gz_header _gz_header
 #endif
 
 #define WINDOW_BITS   15
 
 #ifndef RZ_BLOCK_SIZE
 #define RZ_BLOCK_SIZE (1<<WINDOW_BITS)
 #endif
 
 #ifndef RZ_BUFFER_SIZE
 #define RZ_BUFFER_SIZE 4096
 #endif
 
 #ifndef RZ_COMPRESS_LEVEL
 #define RZ_COMPRESS_LEVEL 6
 #endif
 
 #define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE)
 
 typedef struct {
 	uint32_t *cell_offsets; // i
 	int64_t  *bin_offsets; // i / BIN_SIZE
 	int size;
 	int cap;
 } ZBlockIndex;
 /* When storing index, output bytes in Big-Endian everywhere */
 
 #define FILE_TYPE_RZ	1
 #define FILE_TYPE_PLAIN	2
 #define FILE_TYPE_GZ	3
 
 typedef struct RandomAccessZFile  {
 	char mode; /* 'w' : write mode; 'r' : read mode */
 	int file_type;
 	/* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
 #ifdef _USE_KNETFILE
     union {
         knetFile *fpr;
         int fpw;
     } x;
 #else
 	int filedes; /* the file descriptor */
 #endif
 	z_stream *stream;
 	ZBlockIndex *index;
 	int64_t in, out, end, src_end;
 	/* in: n bytes total in; out: n bytes total out; */
 	/* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
 	int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
 	int64_t block_pos, block_off, next_block_pos;
 	/* block_pos: the start postiion of current block  in compressed file */
 	/* block_off: tell how many bytes have been read from current block */
 	void *inbuf, *outbuf;
 	int header_size;
 	gz_header *header;
 	/* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
 	int buf_off, buf_len;
 	int z_err, z_eof;
 	int seekable;
 	/* Indice where the source is seekable */
 	int load_index;
 	/* set has_index to 0 in mode 'w', then index will be discarded */
 } RAZF;
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
 	RAZF* razf_dopen(int data_fd, const char *mode);
 	RAZF *razf_open(const char *fn, const char *mode);
 	int razf_write(RAZF* rz, const void *data, int size);
 	int razf_read(RAZF* rz, void *data, int size);
 	int64_t razf_seek(RAZF* rz, int64_t pos, int where);
 	void razf_close(RAZF* rz);
 
 #define razf_tell(rz) ((rz)->out)
 
 	RAZF* razf_open2(const char *filename, const char *mode);
 	RAZF* razf_dopen2(int fd, const char *mode);
 	uint64_t razf_tell2(RAZF *rz);
 	int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);
 
 #ifdef __cplusplus
 }
 #endif
 
 #endif