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1 /* The MIT License
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2
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3 Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
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4 2011, 2012 Attractive Chaos <attractor@live.co.uk>
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5
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6 Permission is hereby granted, free of charge, to any person obtaining a copy
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7 of this software and associated documentation files (the "Software"), to deal
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8 in the Software without restriction, including without limitation the rights
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9 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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10 copies of the Software, and to permit persons to whom the Software is
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11 furnished to do so, subject to the following conditions:
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12
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13 The above copyright notice and this permission notice shall be included in
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14 all copies or substantial portions of the Software.
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15
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16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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17 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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18 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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19 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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20 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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21 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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22 THE SOFTWARE.
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23 */
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24
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25 /* The BGZF library was originally written by Bob Handsaker from the Broad
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26 * Institute. It was later improved by the SAMtools developers. */
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27
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28 #ifndef __BGZF_H
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29 #define __BGZF_H
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30
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31 #include <stdint.h>
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32 #include <stdio.h>
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33 #include <zlib.h>
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34 #include <sys/types.h>
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35
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36 #define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
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37 #define BGZF_MAX_BLOCK_SIZE 0x10000
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38
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39 #define BGZF_ERR_ZLIB 1
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40 #define BGZF_ERR_HEADER 2
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41 #define BGZF_ERR_IO 4
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42 #define BGZF_ERR_MISUSE 8
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43
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44 typedef struct {
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45 int errcode:16, is_write:2, compress_level:14;
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46 int cache_size;
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47 int block_length, block_offset;
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48 int64_t block_address;
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49 void *uncompressed_block, *compressed_block;
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50 void *cache; // a pointer to a hash table
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51 void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading
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52 void *mt; // only used for multi-threading
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53 } BGZF;
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54
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55 #ifndef KSTRING_T
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56 #define KSTRING_T kstring_t
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57 typedef struct __kstring_t {
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58 size_t l, m;
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59 char *s;
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60 } kstring_t;
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61 #endif
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62
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63 #ifdef __cplusplus
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64 extern "C" {
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65 #endif
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66
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67 /******************
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68 * Basic routines *
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69 ******************/
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70
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71 /**
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72 * Open an existing file descriptor for reading or writing.
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73 *
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74 * @param fd file descriptor
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75 * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
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76 * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
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77 * @return BGZF file handler; 0 on error
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78 */
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79 BGZF* bgzf_dopen(int fd, const char *mode);
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80
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81 #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
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82
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83 /**
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84 * Open the specified file for reading or writing.
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85 */
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86 BGZF* bgzf_open(const char* path, const char *mode);
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87
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88 /**
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89 * Close the BGZF and free all associated resources.
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90 *
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91 * @param fp BGZF file handler
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92 * @return 0 on success and -1 on error
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93 */
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94 int bgzf_close(BGZF *fp);
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95
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96 /**
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97 * Read up to _length_ bytes from the file storing into _data_.
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98 *
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99 * @param fp BGZF file handler
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100 * @param data data array to read into
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101 * @param length size of data to read
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102 * @return number of bytes actually read; 0 on end-of-file and -1 on error
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103 */
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104 ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length);
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105
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106 /**
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107 * Write _length_ bytes from _data_ to the file.
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108 *
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109 * @param fp BGZF file handler
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110 * @param data data array to write
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111 * @param length size of data to write
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112 * @return number of bytes actually written; -1 on error
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113 */
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114 ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length);
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115
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116 /**
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117 * Write the data in the buffer to the file.
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118 */
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119 int bgzf_flush(BGZF *fp);
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120
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121 /**
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122 * Return a virtual file pointer to the current location in the file.
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123 * No interpetation of the value should be made, other than a subsequent
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124 * call to bgzf_seek can be used to position the file at the same point.
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125 * Return value is non-negative on success.
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126 */
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127 #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
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128
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129 /**
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130 * Set the file to read from the location specified by _pos_.
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131 *
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132 * @param fp BGZF file handler
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133 * @param pos virtual file offset returned by bgzf_tell()
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134 * @param whence must be SEEK_SET
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135 * @return 0 on success and -1 on error
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136 */
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137 int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);
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138
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139 /**
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140 * Check if the BGZF end-of-file (EOF) marker is present
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141 *
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142 * @param fp BGZF file handler opened for reading
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143 * @return 1 if EOF is present; 0 if not or on I/O error
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144 */
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145 int bgzf_check_EOF(BGZF *fp);
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146
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147 /**
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148 * Check if a file is in the BGZF format
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149 *
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150 * @param fn file name
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151 * @return 1 if _fn_ is BGZF; 0 if not or on I/O error
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152 */
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153 int bgzf_is_bgzf(const char *fn);
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154
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155 /*********************
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156 * Advanced routines *
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157 *********************/
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158
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159 /**
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160 * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
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161 *
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162 * @param fp BGZF file handler
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163 * @param size size of cache in bytes; 0 to disable caching (default)
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164 */
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165 void bgzf_set_cache_size(BGZF *fp, int size);
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166
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167 /**
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168 * Flush the file if the remaining buffer size is smaller than _size_
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169 */
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170 int bgzf_flush_try(BGZF *fp, ssize_t size);
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171
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172 /**
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173 * Read one byte from a BGZF file. It is faster than bgzf_read()
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174 * @param fp BGZF file handler
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175 * @return byte read; -1 on end-of-file or error
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176 */
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177 int bgzf_getc(BGZF *fp);
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178
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179 /**
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180 * Read one line from a BGZF file. It is faster than bgzf_getc()
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181 *
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182 * @param fp BGZF file handler
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183 * @param delim delimitor
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184 * @param str string to write to; must be initialized
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185 * @return length of the string; 0 on end-of-file; negative on error
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186 */
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187 int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
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188
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189 /**
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190 * Read the next BGZF block.
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191 */
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192 int bgzf_read_block(BGZF *fp);
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193
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194 /**
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195 * Enable multi-threading (only effective on writing)
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196 *
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197 * @param fp BGZF file handler; must be opened for writing
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198 * @param n_threads #threads used for writing
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199 * @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended
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200 */
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201 int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks);
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202
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203 #ifdef __cplusplus
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204 }
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205 #endif
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206
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207 #endif
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