1 /*
2 Copyright (c) 2012-2013 Genome Research Ltd.
3 Author: James Bonfield <jkb@sanger.ac.uk>
4
5 Redistribution and use in source and binary forms, with or without
6 modification, are permitted provided that the following conditions are met:
7
8 1. Redistributions of source code must retain the above copyright notice,
9 this list of conditions and the following disclaimer.
10
11 2. Redistributions in binary form must reproduce the above copyright notice,
12 this list of conditions and the following disclaimer in the documentation
13 and/or other materials provided with the distribution.
14
15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
16 Institute nor the names of its contributors may be used to endorse or promote
17 products derived from this software without specific prior written permission.
18
19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD 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 OR
25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30
31 #ifndef _CRAM_ENCODINGS_H_
32 #define _CRAM_ENCODINGS_H_
33
34 #include <inttypes.h>
35
36 #ifdef __cplusplus
37 extern "C" {
38 #endif
39
40 struct cram_codec;
41
42 /*
43 * Slow but simple huffman decoder to start with.
44 * Read a bit at a time, keeping track of {length, value}
45 * eg. 1 1 0 1 => {1,1}, {2,3}, {3,6}, {4,13}
46 *
47 * Keep track of this through the huffman code table.
48 * For fast scanning we have an index of where the first code of length X
49 * appears.
50 */
51 typedef struct {
52 int32_t symbol;
53 int32_t p; // next code start value, minus index to codes[]
54 int32_t code;
55 int32_t len;
56 } cram_huffman_code;
57
58 typedef struct {
59 int ncodes;
60 cram_huffman_code *codes;
61 } cram_huffman_decoder;
62
63 #define MAX_HUFF 128
64 typedef struct {
65 cram_huffman_code *codes;
66 int nvals;
67 int val2code[MAX_HUFF+1]; // value to code lookup for small values
68 } cram_huffman_encoder;
69
70 typedef struct {
71 int32_t offset;
72 int32_t nbits;
73 } cram_beta_decoder;
74
75 typedef struct {
76 int32_t offset;
77 } cram_gamma_decoder;
78
79 typedef struct {
80 int32_t offset;
81 int32_t k;
82 } cram_subexp_decoder;
83
84 typedef struct {
85 int32_t content_id;
86 enum cram_external_type type;
87 cram_block *b;
88 } cram_external_decoder;
89
90 typedef struct {
91 struct cram_codec *len_codec;
92 struct cram_codec *val_codec;
93 } cram_byte_array_len_decoder;
94
95 typedef struct {
96 unsigned char stop;
97 int32_t content_id;
98 cram_block *b;
99 } cram_byte_array_stop_decoder;
100
101 typedef struct {
102 enum cram_encoding len_encoding;
103 enum cram_encoding val_encoding;
104 void *len_dat;
105 void *val_dat;
106 struct cram_codec *len_codec;
107 struct cram_codec *val_codec;
108 } cram_byte_array_len_encoder;
109
110 /*
111 * A generic codec structure.
112 */
113 typedef struct cram_codec {
114 enum cram_encoding codec;
115 cram_block *out;
116 void (*free)(struct cram_codec *codec);
117 int (*decode)(cram_slice *slice, struct cram_codec *codec,
118 cram_block *in, char *out, int *out_size);
119 int (*encode)(cram_slice *slice, struct cram_codec *codec,
120 char *in, int in_size);
121 int (*store)(struct cram_codec *codec, cram_block *b, char *prefix,
122 int version);
123 void (*reset)(struct cram_codec *codec); // used between slices in a container
124
125 union {
126 cram_huffman_decoder huffman;
127 cram_external_decoder external;
128 cram_beta_decoder beta;
129 cram_gamma_decoder gamma;
130 cram_subexp_decoder subexp;
131 cram_byte_array_len_decoder byte_array_len;
132 cram_byte_array_stop_decoder byte_array_stop;
133
134 cram_huffman_encoder e_huffman;
135 cram_external_decoder e_external;
136 cram_byte_array_stop_decoder e_byte_array_stop;
137 cram_byte_array_len_encoder e_byte_array_len;
138 cram_beta_decoder e_beta;
139 };
140 } cram_codec;
141
142 const char *cram_encoding2str(enum cram_encoding t);
143
144 cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size,
145 enum cram_external_type option,
146 int version);
147 cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st,
148 enum cram_external_type option, void *dat,
149 int version);
150
151 //int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size);
152 //void cram_decoder_free(void *codes);
153
154 //#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++))
155
156 #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)
157
158 /*
159 * Check that enough bits are left in a block to satisy a bit-based decoder.
160 * Return 0 if there are enough
161 * 1 if not.
162 */
163
cram_not_enough_bits(cram_block * blk,int nbits)164 static inline int cram_not_enough_bits(cram_block *blk, int nbits) {
165 if (nbits < 0 ||
166 (blk->byte >= blk->uncomp_size && nbits > 0) ||
167 (blk->uncomp_size - blk->byte <= INT32_MAX / 8 + 1 &&
168 (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
169 return 1;
170 }
171 return 0;
172 }
173
174 /*
175 * Returns the content_id used by this codec, also in id2 if byte_array_len.
176 * Returns -1 for the CORE block and -2 for unneeded.
177 * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
178 */
179 int cram_codec_to_id(cram_codec *c, int *id2);
180
181 /*
182 * cram_codec structures are specialised for decoding or encoding.
183 * Unfortunately this makes turning a decoder into an encoder (such as
184 * when transcoding files) problematic.
185 *
186 * This function converts a cram decoder codec into an encoder version
187 * in-place (ie it modifiers the codec itself).
188 *
189 * Returns 0 on success;
190 * -1 on failure.
191 */
192 int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c);
193
194 #ifdef __cplusplus
195 }
196 #endif
197
198 #endif /* _CRAM_ENCODINGS_H_ */
199