Mercurial > repos > siyuan > prada
view pyPRADA_1.2/tools/samtools-0.1.16/razf.h @ 3:f17965495ec9 draft default tip
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author | siyuan |
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date | Tue, 11 Mar 2014 12:14:01 -0400 |
parents | acc2ca1a3ba4 |
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/*- * RAZF : Random Access compressed(Z) File * Version: 1.0 * Release Date: 2008-10-27 * * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk> * * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF * SUCH DAMAGE. */ #ifndef __RAZF_RJ_H #define __RAZF_RJ_H #include <stdint.h> #include <stdio.h> #include "zlib.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif #if ZLIB_VERNUM < 0x1221 #define _RZ_READONLY struct _gz_header_s; typedef struct _gz_header_s _gz_header; #define gz_header _gz_header #endif #define WINDOW_BITS 15 #ifndef RZ_BLOCK_SIZE #define RZ_BLOCK_SIZE (1<<WINDOW_BITS) #endif #ifndef RZ_BUFFER_SIZE #define RZ_BUFFER_SIZE 4096 #endif #ifndef RZ_COMPRESS_LEVEL #define RZ_COMPRESS_LEVEL 6 #endif #define RZ_BIN_SIZE ((1LLU << 32) / RZ_BLOCK_SIZE) typedef struct { uint32_t *cell_offsets; // i int64_t *bin_offsets; // i / BIN_SIZE int size; int cap; } ZBlockIndex; /* When storing index, output bytes in Big-Endian everywhere */ #define FILE_TYPE_RZ 1 #define FILE_TYPE_PLAIN 2 #define FILE_TYPE_GZ 3 typedef struct RandomAccessZFile { char mode; /* 'w' : write mode; 'r' : read mode */ int file_type; /* plain file or rz file, razf_read support plain file as input too, in this case, razf_read work as buffered fread */ #ifdef _USE_KNETFILE union { knetFile *fpr; int fpw; } x; #else int filedes; /* the file descriptor */ #endif z_stream *stream; ZBlockIndex *index; int64_t in, out, end, src_end; /* in: n bytes total in; out: n bytes total out; */ /* end: the end of all data blocks, while the start of index; src_end: the true end position in uncompressed file */ int buf_flush; // buffer should be flush, suspend inflate util buffer is empty int64_t block_pos, block_off, next_block_pos; /* block_pos: the start postiion of current block in compressed file */ /* block_off: tell how many bytes have been read from current block */ void *inbuf, *outbuf; int header_size; gz_header *header; /* header is used to transfer inflate_state->mode from HEAD to TYPE after call inflateReset */ int buf_off, buf_len; int z_err, z_eof; int seekable; /* Indice where the source is seekable */ int load_index; /* set has_index to 0 in mode 'w', then index will be discarded */ } RAZF; #ifdef __cplusplus extern "C" { #endif RAZF* razf_dopen(int data_fd, const char *mode); RAZF *razf_open(const char *fn, const char *mode); int razf_write(RAZF* rz, const void *data, int size); int razf_read(RAZF* rz, void *data, int size); int64_t razf_seek(RAZF* rz, int64_t pos, int where); void razf_close(RAZF* rz); #define razf_tell(rz) ((rz)->out) RAZF* razf_open2(const char *filename, const char *mode); RAZF* razf_dopen2(int fd, const char *mode); uint64_t razf_tell2(RAZF *rz); int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where); #ifdef __cplusplus } #endif #endif