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1 /*
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2 Copyright (c) 2012-2013 Genome Research Ltd.
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3 Author: James Bonfield <jkb@sanger.ac.uk>
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4
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5 Redistribution and use in source and binary forms, with or without
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6 modification, are permitted provided that the following conditions are met:
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7
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8 1. Redistributions of source code must retain the above copyright notice,
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9 this list of conditions and the following disclaimer.
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10
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11 2. Redistributions in binary form must reproduce the above copyright notice,
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12 this list of conditions and the following disclaimer in the documentation
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13 and/or other materials provided with the distribution.
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14
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15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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16 Institute nor the names of its contributors may be used to endorse or promote
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17 products derived from this software without specific prior written permission.
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18
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19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD 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 OR
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25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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29 */
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30
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31 #ifndef _CRAM_ENCODINGS_H_
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32 #define _CRAM_ENCODINGS_H_
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33
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34 #ifdef __cplusplus
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35 extern "C" {
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36 #endif
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37
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38 #include <inttypes.h>
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39
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40 struct cram_codec;
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41
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42 /*
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43 * Slow but simple huffman decoder to start with.
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44 * Read a bit at a time, keeping track of {length, value}
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45 * eg. 1 1 0 1 => {1,1}, {2,3}, {3,6}, {4,13}
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46 *
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47 * Keep track of this through the huffman code table.
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48 * For fast scanning we have an index of where the first code of length X
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49 * appears.
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50 */
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51 typedef struct {
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52 int32_t symbol;
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53 int32_t p; // next code start value, minus index to codes[]
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54 int32_t code;
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55 int32_t len;
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56 } cram_huffman_code;
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57
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58 typedef struct {
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59 int ncodes;
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60 cram_huffman_code *codes;
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61 } cram_huffman_decoder;
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62
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63 #define MAX_HUFF 128
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64 typedef struct {
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65 cram_huffman_code *codes;
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66 int nvals;
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67 int val2code[MAX_HUFF+1]; // value to code lookup for small values
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68 } cram_huffman_encoder;
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69
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70 typedef struct {
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71 int32_t offset;
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72 int32_t nbits;
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73 } cram_beta_decoder;
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74
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75 typedef struct {
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76 int32_t offset;
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77 } cram_gamma_decoder;
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78
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79 typedef struct {
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80 int32_t offset;
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81 int32_t k;
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82 } cram_subexp_decoder;
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83
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84 typedef struct {
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85 int32_t content_id;
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86 enum cram_external_type type;
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87 } cram_external_decoder;
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88
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89 typedef struct {
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90 struct cram_codec *len_codec;
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91 struct cram_codec *value_codec;
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92 } cram_byte_array_len_decoder;
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93
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94 typedef struct {
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95 unsigned char stop;
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96 int32_t content_id;
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97 } cram_byte_array_stop_decoder;
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98
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99 typedef struct {
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100 enum cram_encoding len_encoding;
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101 enum cram_encoding val_encoding;
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102 void *len_dat;
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103 void *val_dat;
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104 struct cram_codec *len_codec;
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105 struct cram_codec *val_codec;
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106 } cram_byte_array_len_encoder;
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107
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108 /*
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109 * A generic codec structure.
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110 */
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111 typedef struct cram_codec {
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112 enum cram_encoding codec;
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113 cram_block *out;
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114 void (*free)(struct cram_codec *codec);
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115 int (*decode)(cram_slice *slice, struct cram_codec *codec,
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116 cram_block *in, char *out, int *out_size);
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117 int (*encode)(cram_slice *slice, struct cram_codec *codec,
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118 char *in, int in_size);
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119 int (*store)(struct cram_codec *codec, cram_block *b, char *prefix,
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120 int version);
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121 union {
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122 cram_huffman_decoder huffman;
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123 cram_external_decoder external;
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124 cram_beta_decoder beta;
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125 cram_gamma_decoder gamma;
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126 cram_subexp_decoder subexp;
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127 cram_byte_array_len_decoder byte_array_len;
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128 cram_byte_array_stop_decoder byte_array_stop;
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129
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130 cram_huffman_encoder e_huffman;
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131 cram_external_decoder e_external;
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132 cram_byte_array_stop_decoder e_byte_array_stop;
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133 cram_byte_array_len_encoder e_byte_array_len;
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134 cram_beta_decoder e_beta;
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135 };
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136 } cram_codec;
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137
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138 char *cram_encoding2str(enum cram_encoding t);
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139
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140 cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size,
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141 enum cram_external_type option,
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142 int version);
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143 cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st,
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144 enum cram_external_type option, void *dat,
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145 int version);
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146
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147 //int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size);
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148 //void cram_decoder_free(void *codes);
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149
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150 //#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, (--b->bit == -1) && (b->bit = 7, b->byte++))
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151
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152 #define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (--b->bit<0), b->bit&=7)
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153
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154 /*
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155 * Returns the content_id used by this codec, also in id2 if byte_array_len.
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156 * Returns -1 for the CORE block and -2 for unneeded.
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157 * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
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158 */
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159 int cram_codec_to_id(cram_codec *c, int *id2);
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160
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161 #ifdef __cplusplus
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162 }
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163 #endif
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164
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165 #endif /* _CRAM_ENCODINGS_H_ */
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