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_external_decoder;
88
89 typedef struct {
90 struct cram_codec *len_codec;
91 struct cram_codec *val_codec;
92 } cram_byte_array_len_decoder;
93
94 typedef struct {
95 unsigned char stop;
96 int32_t content_id;
97 } cram_byte_array_stop_decoder;
98
99 typedef struct {
100 enum cram_encoding len_encoding;
101 enum cram_encoding val_encoding;
102 void *len_dat;
103 void *val_dat;
104 struct cram_codec *len_codec;
105 struct cram_codec *val_codec;
106 } cram_byte_array_len_encoder;
107
108 /*
109 * A generic codec structure.
110 */
111 #ifdef __SUNPRO_C
112 # pragma error_messages(off, E_ANONYMOUS_UNION_DECL)
113 #endif
114 typedef struct cram_codec {
115 enum cram_encoding codec;
116 cram_block *out;
117 void (*free)(struct cram_codec *codec);
118 int (*decode)(cram_slice *slice, struct cram_codec *codec,
119 cram_block *in, char *out, int *out_size);
120 int (*encode)(cram_slice *slice, struct cram_codec *codec,
121 char *in, int in_size);
122 int (*store)(struct cram_codec *codec, cram_block *b, char *prefix,
123 int version);
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 #ifdef __SUNPRO_C
142 # pragma error_messages(default, E_ANONYMOUS_UNION_DECL)
143 #endif
144
145 const char *cram_encoding2str(enum cram_encoding t);
146
147 cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size,
148 enum cram_external_type option,
149 int version);
150 cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st,
151 enum cram_external_type option, void *dat,
152 int version);
153
154 //int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size);
155 //void cram_decoder_free(void *codes);
156
157 //#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++))
158
159 #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)
160
161 /*
162 * Check that enough bits are left in a block to satisy a bit-based decoder.
163 * Return 0 if there are enough
164 * 1 if not.
165 */
166
cram_not_enough_bits(cram_block * blk,int nbits)167 static inline int cram_not_enough_bits(cram_block *blk, int nbits) {
168 if (nbits < 0 ||
169 (blk->byte >= blk->uncomp_size && nbits > 0) ||
170 (blk->uncomp_size - blk->byte <= INT32_MAX / 8 + 1 &&
171 (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
172 return 1;
173 }
174 return 0;
175 }
176
177 /*
178 * Returns the content_id used by this codec, also in id2 if byte_array_len.
179 * Returns -1 for the CORE block and -2 for unneeded.
180 * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
181 */
182 int cram_codec_to_id(cram_codec *c, int *id2);
183
184 /*
185 * cram_codec structures are specialised for decoding or encoding.
186 * Unfortunately this makes turning a decoder into an encoder (such as
187 * when transcoding files) problematic.
188 *
189 * This function converts a cram decoder codec into an encoder version
190 * in-place (ie it modifiers the codec itself).
191 *
192 * Returns 0 on success;
193 * -1 on failure.
194 */
195 int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c);
196
197 #ifdef __cplusplus
198 }
199 #endif
200
201 #endif /* _CRAM_ENCODINGS_H_ */
202