2 * RAZF : Random Access compressed(Z) File
4 * Release Date: 2008-10-27
6 * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
10 * Redistribution and use in source and binary forms, with or without
11 * modification, are permitted provided that the following conditions
13 * 1. Redistributions of source code must retain the above copyright
14 * notice, this list of conditions and the following disclaimer.
15 * 2. Redistributions in binary form must reproduce the above copyright
16 * notice, this list of conditions and the following disclaimer in the
17 * documentation and/or other materials provided with the distribution.
19 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
20 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
23 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
25 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
26 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
27 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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40 #if ZLIB_VERNUM < 0x1221
43 typedef struct _gz_header_s _gz_header;
44 #define gz_header _gz_header
47 #define WINDOW_BITS 15
50 #define RZ_BLOCK_SIZE (1<<WINDOW_BITS)
53 #ifndef RZ_BUFFER_SIZE
54 #define RZ_BUFFER_SIZE 4096
57 #ifndef RZ_COMPRESS_LEVEL
58 #define RZ_COMPRESS_LEVEL 6
61 #define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE)
64 uint32_t *cell_offsets; // i
65 int64_t *bin_offsets; // i / BIN_SIZE
69 /* When storing index, output bytes in Big-Endian everywhere */
71 #define FILE_TYPE_RZ 1
72 #define FILE_TYPE_PLAIN 2
73 #define FILE_TYPE_GZ 3
75 typedef struct RandomAccessZFile {
76 char mode; /* 'w' : write mode; 'r' : read mode */
78 /* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
79 int filedes; /* the file descriptor */
82 int64_t in, out, end, src_end;
83 /* in: n bytes total in; out: n bytes total out; */
84 /* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
85 int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
86 int64_t block_pos, block_off, next_block_pos;
87 /* block_pos: the start postiion of current block in compressed file */
88 /* block_off: tell how many bytes have been read from current block */
92 /* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
96 /* Indice where the source is seekable */
98 /* set has_index to 0 in mode 'w', then index will be discarded */
105 RAZF* razf_dopen(int data_fd, const char *mode);
106 RAZF *razf_open(const char *fn, const char *mode);
107 int razf_write(RAZF* rz, const void *data, int size);
108 int razf_read(RAZF* rz, void *data, int size);
109 int64_t razf_seek(RAZF* rz, int64_t pos, int where);
110 void razf_close(RAZF* rz);
112 #define razf_tell(rz) ((rz)->out)
114 RAZF* razf_open2(const char *filename, const char *mode);
115 RAZF* razf_dopen2(int fd, const char *mode);
116 uint64_t razf_tell2(RAZF *rz);
117 int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);