0
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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
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5 Permission is hereby granted, free of charge, to any person obtaining a copy
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6 of this software and associated documentation files (the "Software"), to deal
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7 in the Software without restriction, including without limitation the rights
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8 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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9 copies of the Software, and to permit persons to whom the Software is
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10 furnished to do so, subject to the following conditions:
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11
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12 The above copyright notice and this permission notice shall be included in
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13 all copies or substantial portions of the Software.
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14
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15 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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16 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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17 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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18 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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19 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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20 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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21 THE SOFTWARE.
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22 */
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23
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24 #ifndef __BGZF_H
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25 #define __BGZF_H
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26
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27 #include <stdint.h>
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28 #include <stdio.h>
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29 #include <stdbool.h>
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30 #include <zlib.h>
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31 #ifdef _USE_KNETFILE
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32 #include "knetfile.h"
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33 #endif
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34
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35 //typedef int8_t bool;
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36
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37 typedef struct {
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38 int file_descriptor;
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39 char open_mode; // 'r' or 'w'
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40 bool owned_file, is_uncompressed;
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41 #ifdef _USE_KNETFILE
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42 union {
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43 knetFile *fpr;
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44 FILE *fpw;
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45 } x;
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46 #else
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47 FILE* file;
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48 #endif
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49 int uncompressed_block_size;
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50 int compressed_block_size;
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51 void* uncompressed_block;
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52 void* compressed_block;
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53 int64_t block_address;
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54 int block_length;
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55 int block_offset;
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56 int cache_size;
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57 const char* error;
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58 void *cache; // a pointer to a hash table
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59 } BGZF;
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60
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61 #ifdef __cplusplus
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62 extern "C" {
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63 #endif
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64
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65 /*
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66 * Open an existing file descriptor for reading or writing.
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67 * Mode must be either "r" or "w".
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68 * A subsequent bgzf_close will not close the file descriptor.
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69 * Returns null on error.
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70 */
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71 BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
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72
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73 /*
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74 * Open the specified file for reading or writing.
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75 * Mode must be either "r" or "w".
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76 * Returns null on error.
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77 */
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78 BGZF* bgzf_open(const char* path, const char* __restrict mode);
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79
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80 /*
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81 * Close the BGZ file and free all associated resources.
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82 * Does not close the underlying file descriptor if created with bgzf_fdopen.
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83 * Returns zero on success, -1 on error.
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84 */
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85 int bgzf_close(BGZF* fp);
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86
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87 /*
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88 * Read up to length bytes from the file storing into data.
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89 * Returns the number of bytes actually read.
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90 * Returns zero on end of file.
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91 * Returns -1 on error.
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92 */
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93 int bgzf_read(BGZF* fp, void* data, int length);
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94
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95 /*
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96 * Write length bytes from data to the file.
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97 * Returns the number of bytes written.
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98 * Returns -1 on error.
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99 */
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100 int bgzf_write(BGZF* fp, const void* data, int length);
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101
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102 /*
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103 * Return a virtual file pointer to the current location in the file.
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104 * No interpetation of the value should be made, other than a subsequent
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105 * call to bgzf_seek can be used to position the file at the same point.
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106 * Return value is non-negative on success.
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107 * Returns -1 on error.
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108 */
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109 int64_t bgzf_tell(BGZF* fp);
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110
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111 /*
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112 * Set the file to read from the location specified by pos, which must
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113 * be a value previously returned by bgzf_tell for this file (but not
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114 * necessarily one returned by this file handle).
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115 * The where argument must be SEEK_SET.
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116 * Seeking on a file opened for write is not supported.
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117 * Returns zero on success, -1 on error.
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118 */
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119 int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
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120
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121 /*
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122 * Set the cache size. Zero to disable. By default, caching is
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123 * disabled. The recommended cache size for frequent random access is
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124 * about 8M bytes.
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125 */
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126 void bgzf_set_cache_size(BGZF *fp, int cache_size);
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127
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128 int bgzf_check_EOF(BGZF *fp);
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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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