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comparison ezBAMQC/src/htslib/cram/cram_codecs.h @ 0:dfa3745e5fd8

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date Thu, 24 Mar 2016 17:12:52 -0400
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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 #ifdef __cplusplus
35 extern "C" {
36 #endif
37
38 #include <inttypes.h>
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 *value_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 typedef struct cram_codec {
112 enum cram_encoding codec;
113 cram_block *out;
114 void (*free)(struct cram_codec *codec);
115 int (*decode)(cram_slice *slice, struct cram_codec *codec,
116 cram_block *in, char *out, int *out_size);
117 int (*encode)(cram_slice *slice, struct cram_codec *codec,
118 char *in, int in_size);
119 int (*store)(struct cram_codec *codec, cram_block *b, char *prefix,
120 int version);
121 union {
122 cram_huffman_decoder huffman;
123 cram_external_decoder external;
124 cram_beta_decoder beta;
125 cram_gamma_decoder gamma;
126 cram_subexp_decoder subexp;
127 cram_byte_array_len_decoder byte_array_len;
128 cram_byte_array_stop_decoder byte_array_stop;
129
130 cram_huffman_encoder e_huffman;
131 cram_external_decoder e_external;
132 cram_byte_array_stop_decoder e_byte_array_stop;
133 cram_byte_array_len_encoder e_byte_array_len;
134 cram_beta_decoder e_beta;
135 };
136 } cram_codec;
137
138 char *cram_encoding2str(enum cram_encoding t);
139
140 cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size,
141 enum cram_external_type option,
142 int version);
143 cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st,
144 enum cram_external_type option, void *dat,
145 int version);
146
147 //int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size);
148 //void cram_decoder_free(void *codes);
149
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++))
151
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)
153
154 /*
155 * Returns the content_id used by this codec, also in id2 if byte_array_len.
156 * Returns -1 for the CORE block and -2 for unneeded.
157 * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
158 */
159 int cram_codec_to_id(cram_codec *c, int *id2);
160
161 #ifdef __cplusplus
162 }
163 #endif
164
165 #endif /* _CRAM_ENCODINGS_H_ */