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

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 /*-
 * RAZF : Random Access compressed(Z) File
 * Version: 1.0
 * Release Date: 2008-10-27
 *
 * Copyright 2008, Jue Ruan <[e-mail]>, Heng Li <[e-mail]>
 *
 * 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