BGI/SOAPdenovo2/standardPregraph/inc/razf.h

   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 {
  69         uint32_t * cell_offsets; // i
  70         int64_t * bin_offsets; // i / BIN_SIZE
  71         int size;
  72         int cap;
  73 } ZBlockIndex;
  74 /* When storing index, output bytes in Big-Endian everywhere */
  75
  76 #define FILE_TYPE_RZ    1
  77 #define FILE_TYPE_PLAIN 2
  78 #define FILE_TYPE_GZ    3
  79
  80 typedef struct RandomAccessZFile
  81 {
  82         char mode; /* 'w' : write mode; 'r' : read mode */
  83         int file_type;
  84         /* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */
  85 #ifdef _USE_KNETFILE
  86         union
  87         {
  88                 knetFile * fpr;
  89                 int fpw;
  90         } x;
  91 #else
  92         int filedes; /* the file descriptor */
  93 #endif
  94         z_stream * stream;
  95         ZBlockIndex * index;
  96         int64_t in, out, end, src_end;
  97         /* in: n bytes total in; out: n bytes total out; */
  98         /* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */
  99         int buf_flush; // buffer should be flush, suspend inflate util buffer is empty
 100         int64_t block_pos, block_off, next_block_pos;
 101         /* block_pos: the start postiion of current block  in compressed file */
 102         /* block_off: tell how many bytes have been read from current block */
 103         void * inbuf, *outbuf;
 104         int header_size;
 105         gz_header * header;
 106         /* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */
 107         int buf_off, buf_len;
 108         int z_err, z_eof;
 109         int seekable;
 110         /* Indice where the source is seekable */
 111         int load_index;
 112         /* set has_index to 0 in mode 'w', then index will be discarded */
 113 } RAZF;
 114
 115 #ifdef __cplusplus
 116 extern "C" {
 117 #endif
 118
 119         RAZF * razf_dopen ( int data_fd, const char * mode );
 120         RAZF * razf_open ( const char * fn, const char * mode );
 121         int razf_write ( RAZF * rz, const void * data, int size );
 122         int razf_read ( RAZF * rz, void * data, int size );
 123         int64_t razf_seek ( RAZF * rz, int64_t pos, int where );
 124         void razf_close ( RAZF * rz );
 125
 126 #define razf_tell(rz) ((rz)->out)
 127
 128         RAZF * razf_open2 ( const char * filename, const char * mode );
 129         RAZF * razf_dopen2 ( int fd, const char * mode );
 130         uint64_t razf_tell2 ( RAZF * rz );
 131         int64_t razf_seek2 ( RAZF * rz, uint64_t voffset, int where );
 132
 133 #ifdef __cplusplus
 134 }
 135 #endif
 136
 137 #endif