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1 /*-
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2 * RAZF : Random Access compressed(Z) File
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3 * Version: 1.0
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4 * Release Date: 2008-10-27
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5 *
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6 * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
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7 *
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8 * All rights reserved.
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9 *
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10 * Redistribution and use in source and binary forms, with or without
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11 * modification, are permitted provided that the following conditions
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12 * are met:
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13 * 1. Redistributions of source code must retain the above copyright
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14 * notice, this list of conditions and the following disclaimer.
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15 * 2. Redistributions in binary form must reproduce the above copyright
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16 * notice, this list of conditions and the following disclaimer in the
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17 * documentation and/or other materials provided with the distribution.
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18 *
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19 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
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20 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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22 * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
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23 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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24 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
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25 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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26 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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27 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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28 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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29 * SUCH DAMAGE.
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30 */
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31
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32
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33 #ifndef __RAZF_RJ_H
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34 #define __RAZF_RJ_H
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35
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36 #include <stdint.h>
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37 #include <stdio.h>
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38 #include "zlib.h"
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39
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40 #ifdef _USE_KNETFILE
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41 #include "knetfile.h"
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42 #endif
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43
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44 #if ZLIB_VERNUM < 0x1221
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45 #define _RZ_READONLY
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46 struct _gz_header_s;
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47 typedef struct _gz_header_s _gz_header;
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48 #define gz_header _gz_header
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49 #endif
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50
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51 #define WINDOW_BITS 15
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52
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53 #ifndef RZ_BLOCK_SIZE
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54 #define RZ_BLOCK_SIZE (1<<WINDOW_BITS)
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55 #endif
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56
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57 #ifndef RZ_BUFFER_SIZE
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58 #define RZ_BUFFER_SIZE 4096
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59 #endif
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60
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61 #ifndef RZ_COMPRESS_LEVEL
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62 #define RZ_COMPRESS_LEVEL 6
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63 #endif
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64
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65 #define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE)
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66
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67 typedef struct {
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68 uint32_t *cell_offsets; // i
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69 int64_t *bin_offsets; // i / BIN_SIZE
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70 int size;
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71 int cap;
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72 } ZBlockIndex;
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73 /* When storing index, output bytes in Big-Endian everywhere */
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74
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75 #define FILE_TYPE_RZ 1
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76 #define FILE_TYPE_PLAIN 2
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77 #define FILE_TYPE_GZ 3
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78
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79 typedef struct RandomAccessZFile {
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80 char mode; /* 'w' : write mode; 'r' : read mode */
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81 int file_type;
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82 /* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
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83 #ifdef _USE_KNETFILE
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84 union {
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85 knetFile *fpr;
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86 int fpw;
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87 } x;
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88 #else
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89 int filedes; /* the file descriptor */
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90 #endif
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91 z_stream *stream;
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92 ZBlockIndex *index;
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93 int64_t in, out, end, src_end;
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94 /* in: n bytes total in; out: n bytes total out; */
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95 /* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
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96 int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
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97 int64_t block_pos, block_off, next_block_pos;
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98 /* block_pos: the start postiion of current block in compressed file */
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99 /* block_off: tell how many bytes have been read from current block */
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100 void *inbuf, *outbuf;
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101 int header_size;
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102 gz_header *header;
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103 /* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
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104 int buf_off, buf_len;
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105 int z_err, z_eof;
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106 int seekable;
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107 /* Indice where the source is seekable */
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108 int load_index;
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109 /* set has_index to 0 in mode 'w', then index will be discarded */
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110 } RAZF;
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111
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112 #ifdef __cplusplus
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113 extern "C" {
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114 #endif
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115
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116 RAZF* razf_dopen(int data_fd, const char *mode);
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117 RAZF *razf_open(const char *fn, const char *mode);
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118 int razf_write(RAZF* rz, const void *data, int size);
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119 int razf_read(RAZF* rz, void *data, int size);
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120 int64_t razf_seek(RAZF* rz, int64_t pos, int where);
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121 void razf_close(RAZF* rz);
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122
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123 #define razf_tell(rz) ((rz)->out)
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124
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125 RAZF* razf_open2(const char *filename, const char *mode);
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126 RAZF* razf_dopen2(int fd, const char *mode);
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127 uint64_t razf_tell2(RAZF *rz);
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128 int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);
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129
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130 #ifdef __cplusplus
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131 }
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132 #endif
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133
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134 #endif
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