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comparison pyPRADA_1.2/tools/samtools-0.1.16/razf.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 /*-
2 * RAZF : Random Access compressed(Z) File
3 * Version: 1.0
4 * Release Date: 2008-10-27
5 *
6 * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
7 *
8 * All rights reserved.
9 *
10 * Redistribution and use in source and binary forms, with or without
11 * modification, are permitted provided that the following conditions
12 * are met:
13 * 1. Redistributions of source code must retain the above copyright
14 * notice, this list of conditions and the following disclaimer.
15 * 2. Redistributions in binary form must reproduce the above copyright
16 * notice, this list of conditions and the following disclaimer in the
17 * documentation and/or other materials provided with the distribution.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
20 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR 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
25 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
26 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
27 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
28 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
29 * SUCH DAMAGE.
30 */
31
32
33 #ifndef __RAZF_RJ_H
34 #define __RAZF_RJ_H
35
36 #include <stdint.h>
37 #include <stdio.h>
38 #include "zlib.h"
39
40 #ifdef _USE_KNETFILE
41 #include "knetfile.h"
42 #endif
43
44 #if ZLIB_VERNUM < 0x1221
45 #define _RZ_READONLY
46 struct _gz_header_s;
47 typedef struct _gz_header_s _gz_header;
48 #define gz_header _gz_header
49 #endif
50
51 #define WINDOW_BITS 15
52
53 #ifndef RZ_BLOCK_SIZE
54 #define RZ_BLOCK_SIZE (1<<WINDOW_BITS)
55 #endif
56
57 #ifndef RZ_BUFFER_SIZE
58 #define RZ_BUFFER_SIZE 4096
59 #endif
60
61 #ifndef RZ_COMPRESS_LEVEL
62 #define RZ_COMPRESS_LEVEL 6
63 #endif
64
65 #define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE)
66
67 typedef struct {
68 uint32_t *cell_offsets; // i
69 int64_t *bin_offsets; // i / BIN_SIZE
70 int size;
71 int cap;
72 } ZBlockIndex;
73 /* When storing index, output bytes in Big-Endian everywhere */
74
75 #define FILE_TYPE_RZ 1
76 #define FILE_TYPE_PLAIN 2
77 #define FILE_TYPE_GZ 3
78
79 typedef struct RandomAccessZFile {
80 char mode; /* 'w' : write mode; 'r' : read mode */
81 int file_type;
82 /* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
83 #ifdef _USE_KNETFILE
84 union {
85 knetFile *fpr;
86 int fpw;
87 } x;
88 #else
89 int filedes; /* the file descriptor */
90 #endif
91 z_stream *stream;
92 ZBlockIndex *index;
93 int64_t in, out, end, src_end;
94 /* in: n bytes total in; out: n bytes total out; */
95 /* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
96 int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
97 int64_t block_pos, block_off, next_block_pos;
98 /* block_pos: the start postiion of current block in compressed file */
99 /* block_off: tell how many bytes have been read from current block */
100 void *inbuf, *outbuf;
101 int header_size;
102 gz_header *header;
103 /* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
104 int buf_off, buf_len;
105 int z_err, z_eof;
106 int seekable;
107 /* Indice where the source is seekable */
108 int load_index;
109 /* set has_index to 0 in mode 'w', then index will be discarded */
110 } RAZF;
111
112 #ifdef __cplusplus
113 extern "C" {
114 #endif
115
116 RAZF* razf_dopen(int data_fd, const char *mode);
117 RAZF *razf_open(const char *fn, const char *mode);
118 int razf_write(RAZF* rz, const void *data, int size);
119 int razf_read(RAZF* rz, void *data, int size);
120 int64_t razf_seek(RAZF* rz, int64_t pos, int where);
121 void razf_close(RAZF* rz);
122
123 #define razf_tell(rz) ((rz)->out)
124
125 RAZF* razf_open2(const char *filename, const char *mode);
126 RAZF* razf_dopen2(int fd, const char *mode);
127 uint64_t razf_tell2(RAZF *rz);
128 int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);
129
130 #ifdef __cplusplus
131 }
132 #endif
133
134 #endif