X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Frazf.c;fp=samtools%2Frazf.c;h=0000000000000000000000000000000000000000;hp=e7499f9f61e6c2fae4ec71a5f4a500ed5b151fe8;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/razf.c b/samtools/razf.c
deleted file mode 100644
index e7499f9..0000000
--- a/samtools/razf.c
+++ /dev/null
@@ -1,853 +0,0 @@
-/*
- * 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 _NO_RAZF
-
-#include <fcntl.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-#include "razf.h"
-
-
-#if ZLIB_VERNUM < 0x1221
-struct _gz_header_s {
-    int     text;
-    uLong   time;
-    int     xflags;
-    int     os;
-    Bytef   *extra;
-    uInt    extra_len;
-    uInt    extra_max;
-    Bytef   *name;
-    uInt    name_max;
-    Bytef   *comment;
-    uInt    comm_max;
-    int     hcrc;
-    int     done;
-};
-#warning "zlib < 1.2.2.1; RAZF writing is disabled."
-#endif
-
-#define DEF_MEM_LEVEL 8
-
-static inline uint32_t byte_swap_4(uint32_t v){
-	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
-	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
-}
-
-static inline uint64_t byte_swap_8(uint64_t v){
-	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
-	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
-	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
-}
-
-static inline int is_big_endian(){
-	int x = 0x01;
-	char *c = (char*)&x;
-	return (c[0] != 0x01);
-}
-
-#ifndef _RZ_READONLY
-static void add_zindex(RAZF *rz, int64_t in, int64_t out){
-	if(rz->index->size == rz->index->cap){
-		rz->index->cap = rz->index->cap * 1.5 + 2;
-		rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
-		rz->index->bin_offsets  = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
-	}
-	if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
-	rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
-	rz->index->size ++;
-}
-
-static void save_zindex(RAZF *rz, int fd){
-	int32_t i, v32;
-	int is_be;
-	is_be = is_big_endian();
-	if(is_be) write(fd, &rz->index->size, sizeof(int));
-	else {
-		v32 = byte_swap_4((uint32_t)rz->index->size);
-		write(fd, &v32, sizeof(uint32_t));
-	}
-	v32 = rz->index->size / RZ_BIN_SIZE + 1;
-	if(!is_be){
-		for(i=0;i<v32;i++) rz->index->bin_offsets[i]  = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
-		for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
-	}
-	write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
-	write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
-}
-#endif
-
-#ifdef _USE_KNETFILE
-static void load_zindex(RAZF *rz, knetFile *fp){
-#else
-static void load_zindex(RAZF *rz, int fd){
-#endif
-	int32_t i, v32;
-	int is_be;
-	if(!rz->load_index) return;
-	if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
-	is_be = is_big_endian();
-#ifdef _USE_KNETFILE
-	knet_read(fp, &rz->index->size, sizeof(int));
-#else
-	read(fd, &rz->index->size, sizeof(int));
-#endif
-	if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
-	rz->index->cap = rz->index->size;
-	v32 = rz->index->size / RZ_BIN_SIZE + 1;
-	rz->index->bin_offsets  = malloc(sizeof(int64_t) * v32);
-#ifdef _USE_KNETFILE
-	knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
-#else
-	read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
-#endif
-	rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
-#ifdef _USE_KNETFILE
-	knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
-#else
-	read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
-#endif
-	if(!is_be){
-		for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
-		for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
-	}
-}
-
-#ifdef _RZ_READONLY
-static RAZF* razf_open_w(int fd)
-{
-	fprintf(stderr, "[razf_open_w] Writing is not available with zlib ver < 1.2.2.1\n");
-	return 0;
-}
-#else
-static RAZF* razf_open_w(int fd){
-	RAZF *rz;
-#ifdef _WIN32
-	setmode(fd, O_BINARY);
-#endif
-	rz = calloc(1, sizeof(RAZF));
-	rz->mode = 'w';
-#ifdef _USE_KNETFILE
-    rz->x.fpw = fd;
-#else
-	rz->filedes = fd;
-#endif
-	rz->stream = calloc(sizeof(z_stream), 1);
-	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
-	rz->outbuf = malloc(RZ_BUFFER_SIZE);
-	rz->index = calloc(sizeof(ZBlockIndex), 1);
-	deflateInit2(rz->stream, RZ_COMPRESS_LEVEL, Z_DEFLATED, WINDOW_BITS + 16, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY);
-	rz->stream->avail_out = RZ_BUFFER_SIZE;
-	rz->stream->next_out  = rz->outbuf;
-	rz->header = calloc(sizeof(gz_header), 1);
-	rz->header->os    = 0x03; //Unix
-	rz->header->text  = 0;
-	rz->header->time  = 0;
-	rz->header->extra = malloc(7);
-	strncpy((char*)rz->header->extra, "RAZF", 4);
-	rz->header->extra[4] = 1; // obsolete field
-	// block size = RZ_BLOCK_SIZE, Big-Endian
-	rz->header->extra[5] = RZ_BLOCK_SIZE >> 8;
-	rz->header->extra[6] = RZ_BLOCK_SIZE & 0xFF;
-	rz->header->extra_len = 7;
-	rz->header->name = rz->header->comment  = 0;
-	rz->header->hcrc = 0;
-	deflateSetHeader(rz->stream, rz->header);
-	rz->block_pos = rz->block_off = 0;
-	return rz;
-}
-
-static void _razf_write(RAZF* rz, const void *data, int size){
-	int tout;
-	rz->stream->avail_in = size;
-	rz->stream->next_in  = (void*)data;
-	while(1){
-		tout = rz->stream->avail_out;
-		deflate(rz->stream, Z_NO_FLUSH);
-		rz->out += tout - rz->stream->avail_out;
-		if(rz->stream->avail_out) break;
-#ifdef _USE_KNETFILE
-		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#else
-		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#endif
-		rz->stream->avail_out = RZ_BUFFER_SIZE;
-		rz->stream->next_out  = rz->outbuf;
-		if(rz->stream->avail_in == 0) break;
-	};
-	rz->in += size - rz->stream->avail_in;
-	rz->block_off += size - rz->stream->avail_in;
-}
-
-static void razf_flush(RAZF *rz){
-	uint32_t tout;
-	if(rz->buf_len){
-		_razf_write(rz, rz->inbuf, rz->buf_len);
-		rz->buf_off = rz->buf_len = 0;
-	}
-	if(rz->stream->avail_out){
-#ifdef _USE_KNETFILE    
-		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#else        
-		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#endif
-		rz->stream->avail_out = RZ_BUFFER_SIZE;
-		rz->stream->next_out  = rz->outbuf;
-	}
-	while(1){
-		tout = rz->stream->avail_out;
-		deflate(rz->stream, Z_FULL_FLUSH);
-		rz->out += tout - rz->stream->avail_out;
-		if(rz->stream->avail_out == 0){
-#ifdef _USE_KNETFILE    
-			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#else            
-			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#endif
-			rz->stream->avail_out = RZ_BUFFER_SIZE;
-			rz->stream->next_out  = rz->outbuf;
-		} else break;
-	}
-	rz->block_pos = rz->out;
-	rz->block_off = 0;
-}
-
-static void razf_end_flush(RAZF *rz){
-	uint32_t tout;
-	if(rz->buf_len){
-		_razf_write(rz, rz->inbuf, rz->buf_len);
-		rz->buf_off = rz->buf_len = 0;
-	}
-	while(1){
-		tout = rz->stream->avail_out;
-		deflate(rz->stream, Z_FINISH);
-		rz->out += tout - rz->stream->avail_out;
-		if(rz->stream->avail_out < RZ_BUFFER_SIZE){
-#ifdef _USE_KNETFILE        
-			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#else            
-			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
-#endif
-			rz->stream->avail_out = RZ_BUFFER_SIZE;
-			rz->stream->next_out  = rz->outbuf;
-		} else break;
-	}
-}
-
-static void _razf_buffered_write(RAZF *rz, const void *data, int size){
-	int i, n;
-	while(1){
-		if(rz->buf_len == RZ_BUFFER_SIZE){
-			_razf_write(rz, rz->inbuf, rz->buf_len);
-			rz->buf_len = 0;
-		}
-		if(size + rz->buf_len < RZ_BUFFER_SIZE){
-			for(i=0;i<size;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
-			rz->buf_len += size;
-			return;
-		} else {
-			n = RZ_BUFFER_SIZE - rz->buf_len;
-			for(i=0;i<n;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
-			size -= n;
-			data += n;
-			rz->buf_len += n;
-		}
-	}
-}
-
-int razf_write(RAZF* rz, const void *data, int size){
-	int ori_size, n;
-	int64_t next_block;
-	ori_size = size;
-	next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
-	while(rz->in + rz->buf_len + size >= next_block){
-		n = next_block - rz->in - rz->buf_len;
-		_razf_buffered_write(rz, data, n);
-		data += n;
-		size -= n;
-		razf_flush(rz);
-		add_zindex(rz, rz->in, rz->out);
-		next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
-	}
-	_razf_buffered_write(rz, data, size);
-	return ori_size;
-}
-#endif
-
-/* gzip flag byte */
-#define ASCII_FLAG   0x01 /* bit 0 set: file probably ascii text */
-#define HEAD_CRC     0x02 /* bit 1 set: header CRC present */
-#define EXTRA_FIELD  0x04 /* bit 2 set: extra field present */
-#define ORIG_NAME    0x08 /* bit 3 set: original file name present */
-#define COMMENT      0x10 /* bit 4 set: file comment present */
-#define RESERVED     0xE0 /* bits 5..7: reserved */
-
-static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *extra_len){
-	int method, flags, n, len;
-	if(size < 2) return 0;
-	if(data[0] != 0x1f || data[1] != 0x8b) return 0;
-	if(size < 4) return 0;
-	method = data[2];
-	flags  = data[3];
-	if(method != Z_DEFLATED || (flags & RESERVED)) return 0;
-	n = 4 + 6; // Skip 6 bytes
-	*extra_off = n + 2;
-	*extra_len = 0;
-	if(flags & EXTRA_FIELD){
-		if(size < n + 2) return 0;
-		len = ((int)data[n + 1] << 8) | data[n];
-		n += 2;
-		*extra_off = n;
-		while(len){
-			if(n >= size) return 0;
-			n ++;
-			len --;
-		}
-		*extra_len = n - (*extra_off);
-	}
-	if(flags & ORIG_NAME) while(n < size && data[n++]);
-	if(flags & COMMENT) while(n < size && data[n++]);
-	if(flags & HEAD_CRC){
-		if(n + 2 > size) return 0;
-		n += 2;
-	}
-	return n;
-}
-
-#ifdef _USE_KNETFILE
-static RAZF* razf_open_r(knetFile *fp, int _load_index){
-#else
-static RAZF* razf_open_r(int fd, int _load_index){
-#endif
-	RAZF *rz;
-	int ext_off, ext_len;
-	int n, is_be, ret;
-	int64_t end;
-	unsigned char c[] = "RAZF";
-	rz = calloc(1, sizeof(RAZF));
-	rz->mode = 'r';
-#ifdef _USE_KNETFILE
-    rz->x.fpr = fp;
-#else
-#ifdef _WIN32
-	setmode(fd, O_BINARY);
-#endif
-	rz->filedes = fd;
-#endif
-	rz->stream = calloc(sizeof(z_stream), 1);
-	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
-	rz->outbuf = malloc(RZ_BUFFER_SIZE);
-	rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
-#ifdef _USE_KNETFILE
-    n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
-#else
-	n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
-#endif
-	ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len);
-	if(ret == 0){
-		PLAIN_FILE:
-		rz->in = n;
-		rz->file_type = FILE_TYPE_PLAIN;
-		memcpy(rz->outbuf, rz->inbuf, n);
-		rz->buf_len = n;
-		free(rz->stream);
-		rz->stream = NULL;
-		return rz;
-	}
-	rz->header_size = ret;
-	ret = inflateInit2(rz->stream, -WINDOW_BITS);
-	if(ret != Z_OK){ inflateEnd(rz->stream); goto PLAIN_FILE;}
-	rz->stream->avail_in = n - rz->header_size;
-	rz->stream->next_in  = rz->inbuf + rz->header_size;
-	rz->stream->avail_out = RZ_BUFFER_SIZE;
-	rz->stream->next_out  = rz->outbuf;
-	rz->file_type = FILE_TYPE_GZ;
-	rz->in = rz->header_size;
-	rz->block_pos = rz->header_size;
-	rz->next_block_pos = rz->header_size;
-	rz->block_off = 0;
-	if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz;
-	if(((((unsigned char*)rz->inbuf)[ext_off + 5] << 8) | ((unsigned char*)rz->inbuf)[ext_off + 6]) != RZ_BLOCK_SIZE){
-		fprintf(stderr, " -- WARNING: RZ_BLOCK_SIZE is not %d, treat source as gz file.  in %s -- %s:%d --\n", RZ_BLOCK_SIZE, __FUNCTION__, __FILE__, __LINE__);
-		return rz;
-	}
-	rz->load_index = _load_index;
-	rz->file_type = FILE_TYPE_RZ;
-#ifdef _USE_KNETFILE
-	if(knet_seek(fp, -16, SEEK_END) == -1){
-#else
-	if(lseek(fd, -16, SEEK_END) == -1){
-#endif
-		UNSEEKABLE:
-		rz->seekable = 0;
-		rz->index = NULL;
-		rz->src_end = rz->end = 0x7FFFFFFFFFFFFFFFLL;
-	} else {
-		is_be = is_big_endian();
-		rz->seekable = 1;
-#ifdef _USE_KNETFILE
-        knet_read(fp, &end, sizeof(int64_t));
-#else
-		read(fd, &end, sizeof(int64_t));
-#endif        
-		if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end);
-		else rz->src_end = end;
-
-#ifdef _USE_KNETFILE
-		knet_read(fp, &end, sizeof(int64_t));
-#else
-		read(fd, &end, sizeof(int64_t));
-#endif        
-		if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end);
-		else rz->end = end;
-		if(n > rz->end){
-			rz->stream->avail_in -= n - rz->end;
-			n = rz->end;
-		}
-		if(rz->end > rz->src_end){
-#ifdef _USE_KNETFILE
-            knet_seek(fp, rz->in, SEEK_SET);
-#else
-			lseek(fd, rz->in, SEEK_SET);
-#endif
-			goto UNSEEKABLE;
-		}
-#ifdef _USE_KNETFILE
-        knet_seek(fp, rz->end, SEEK_SET);
-		if(knet_tell(fp) != rz->end){
-			knet_seek(fp, rz->in, SEEK_SET);
-#else
-		if(lseek(fd, rz->end, SEEK_SET) != rz->end){
-			lseek(fd, rz->in, SEEK_SET);
-#endif
-			goto UNSEEKABLE;
-		}
-#ifdef _USE_KNETFILE
-		load_zindex(rz, fp);
-		knet_seek(fp, n, SEEK_SET);
-#else
-		load_zindex(rz, fd);
-		lseek(fd, n, SEEK_SET);
-#endif
-	}
-	return rz;
-}
-
-#ifdef _USE_KNETFILE
-RAZF* razf_dopen(int fd, const char *mode){
-    if (strstr(mode, "r")) fprintf(stderr,"[razf_dopen] implement me\n");
-    else if(strstr(mode, "w")) return razf_open_w(fd);
-	return NULL;
-}
-
-RAZF* razf_dopen2(int fd, const char *mode)
-{
-    fprintf(stderr,"[razf_dopen2] implement me\n");
-    return NULL;
-}
-#else
-RAZF* razf_dopen(int fd, const char *mode){
-	if(strstr(mode, "r")) return razf_open_r(fd, 1);
-	else if(strstr(mode, "w")) return razf_open_w(fd);
-	else return NULL;
-}
-
-RAZF* razf_dopen2(int fd, const char *mode)
-{
-	if(strstr(mode, "r")) return razf_open_r(fd, 0);
-	else if(strstr(mode, "w")) return razf_open_w(fd);
-	else return NULL;
-}
-#endif
-
-static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){
-	int fd;
-	RAZF *rz;
-	if(strstr(mode, "r")){
-#ifdef _USE_KNETFILE
-        knetFile *fd = knet_open(filename, "r");
-        if (fd == 0) {
-            fprintf(stderr, "[_razf_open] fail to open %s\n", filename);
-            return NULL;
-        }
-#else
-#ifdef _WIN32
-		fd = open(filename, O_RDONLY | O_BINARY);
-#else
-		fd = open(filename, O_RDONLY);
-#endif
-#endif
-		if(fd < 0) return NULL;
-		rz = razf_open_r(fd, _load_index);
-	} else if(strstr(mode, "w")){
-#ifdef _WIN32
-		fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666);
-#else
-		fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666);
-#endif
-		if(fd < 0) return NULL;
-		rz = razf_open_w(fd);
-	} else return NULL;
-	return rz;
-}
-
-RAZF* razf_open(const char *filename, const char *mode){
-	return _razf_open(filename, mode, 1);
-}
-
-RAZF* razf_open2(const char *filename, const char *mode){
-	return _razf_open(filename, mode, 0);
-}
-
-int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){
-	int64_t n;
-	if(rz->mode != 'r' && rz->mode != 'R') return 0;
-	switch(rz->file_type){
-		case FILE_TYPE_PLAIN:
-			if(rz->end == 0x7fffffffffffffffLL){
-#ifdef _USE_KNETFILE
-				if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0;
-                n = knet_tell(rz->x.fpr);
-				knet_seek(rz->x.fpr, 0, SEEK_END);
-                rz->end = knet_tell(rz->x.fpr);
-				knet_seek(rz->x.fpr, n, SEEK_SET);
-#else
-				if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0;
-				rz->end = lseek(rz->filedes, 0, SEEK_END);
-				lseek(rz->filedes, n, SEEK_SET);
-#endif                
-			}
-			*u_size = *c_size = rz->end;
-			return 1;
-		case FILE_TYPE_GZ:
-			return 0;
-		case FILE_TYPE_RZ:
-			if(rz->src_end == rz->end) return 0;
-			*u_size = rz->src_end;
-			*c_size = rz->end;
-			return 1;
-		default:
-			return 0;
-	}
-}
-
-static int _razf_read(RAZF* rz, void *data, int size){
-	int ret, tin;
-	if(rz->z_eof || rz->z_err) return 0;
-	if (rz->file_type == FILE_TYPE_PLAIN) {
-#ifdef _USE_KNETFILE
-		ret = knet_read(rz->x.fpr, data, size);
-#else
-		ret = read(rz->filedes, data, size);
-#endif        
-		if (ret == 0) rz->z_eof = 1;
-		return ret;
-	}
-	rz->stream->avail_out = size;
-	rz->stream->next_out  = data;
-	while(rz->stream->avail_out){
-		if(rz->stream->avail_in == 0){
-			if(rz->in >= rz->end){ rz->z_eof = 1; break; }
-			if(rz->end - rz->in < RZ_BUFFER_SIZE){
-#ifdef _USE_KNETFILE
-				rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
-#else
-				rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in);
-#endif        
-			} else {
-#ifdef _USE_KNETFILE
-				rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
-#else
-				rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
-#endif        
-			}
-			if(rz->stream->avail_in == 0){
-				rz->z_eof = 1;
-				break;
-			}
-			rz->stream->next_in = rz->inbuf;
-		}
-		tin = rz->stream->avail_in;
-		ret = inflate(rz->stream, Z_BLOCK);
-		rz->in += tin - rz->stream->avail_in;
-		if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){
-			fprintf(stderr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
-			rz->z_err = 1;
-			break;
-		}
-		if(ret == Z_STREAM_END){
-			rz->z_eof = 1;
-			break;
-		}
-		if ((rz->stream->data_type&128) && !(rz->stream->data_type&64)){
-			rz->buf_flush = 1;
-			rz->next_block_pos = rz->in;
-			break;
-		}
-	}
-	return size - rz->stream->avail_out;
-}
-
-int razf_read(RAZF *rz, void *data, int size){
-	int ori_size, i;
-	ori_size = size;
-	while(size > 0){
-		if(rz->buf_len){
-			if(size < rz->buf_len){
-				for(i=0;i<size;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
-				rz->buf_off += size;
-				rz->buf_len -= size;
-				data += size;
-				rz->block_off += size;
-				size = 0;
-				break;
-			} else {
-				for(i=0;i<rz->buf_len;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
-				data += rz->buf_len;
-				size -= rz->buf_len;
-				rz->block_off += rz->buf_len;
-				rz->buf_off = 0;
-				rz->buf_len = 0;
-				if(rz->buf_flush){
-					rz->block_pos = rz->next_block_pos;
-					rz->block_off = 0;
-					rz->buf_flush = 0;
-				}
-			}
-		} else if(rz->buf_flush){
-			rz->block_pos = rz->next_block_pos;
-			rz->block_off = 0;
-			rz->buf_flush = 0;
-		}
-		if(rz->buf_flush) continue;
-		rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
-		if(rz->z_eof && rz->buf_len == 0) break;
-	}
-	rz->out += ori_size - size;
-	return ori_size - size;
-}
-
-int razf_skip(RAZF* rz, int size){
-	int ori_size;
-	ori_size = size;
-	while(size > 0){
-		if(rz->buf_len){
-			if(size < rz->buf_len){
-				rz->buf_off += size;
-				rz->buf_len -= size;
-				rz->block_off += size;
-				size = 0;
-				break;
-			} else {
-				size -= rz->buf_len;
-				rz->buf_off = 0;
-				rz->buf_len = 0;
-				rz->block_off += rz->buf_len;
-				if(rz->buf_flush){
-					rz->block_pos = rz->next_block_pos;
-					rz->block_off = 0;
-					rz->buf_flush = 0;
-				}
-			}
-		} else if(rz->buf_flush){
-			rz->block_pos = rz->next_block_pos;
-			rz->block_off = 0;
-			rz->buf_flush = 0;
-		}
-		if(rz->buf_flush) continue;
-		rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
-		if(rz->z_eof || rz->z_err) break;
-	}
-	rz->out += ori_size - size;
-	return ori_size - size;
-}
-
-static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){
-#ifdef _USE_KNETFILE
-	knet_seek(rz->x.fpr, in, SEEK_SET);
-#else
-	lseek(rz->filedes, in, SEEK_SET);
-#endif
-	rz->in  = in;
-	rz->out = out;
-	rz->block_pos = in;
-	rz->next_block_pos = in;
-	rz->block_off = 0;
-	rz->buf_flush = 0;
-	rz->z_eof = rz->z_err = 0;
-	inflateReset(rz->stream);
-	rz->stream->avail_in = 0;
-	rz->buf_off = rz->buf_len = 0;
-}
-
-int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){
-	int64_t pos;
-	rz->z_eof = 0;
-	if(rz->file_type == FILE_TYPE_PLAIN){
-		rz->buf_off = rz->buf_len = 0;
-		pos = block_start + block_offset;
-#ifdef _USE_KNETFILE
-		knet_seek(rz->x.fpr, pos, SEEK_SET);
-        pos = knet_tell(rz->x.fpr);
-#else
-		pos = lseek(rz->filedes, pos, SEEK_SET);
-#endif
-		rz->out = rz->in = pos;
-		return pos;
-	}
-	if(block_start == rz->block_pos && block_offset >= rz->block_off) {
-		block_offset -= rz->block_off;
-		goto SKIP; // Needn't reset inflate
-	}
-	if(block_start  == 0) block_start = rz->header_size; // Automaticly revist wrong block_start
-	_razf_reset_read(rz, block_start, 0);
-	SKIP:
-	if(block_offset) razf_skip(rz, block_offset);
-	return rz->block_off;
-}
-
-int64_t razf_seek(RAZF* rz, int64_t pos, int where){
-	int64_t idx;
-	int64_t seek_pos, new_out;
-	rz->z_eof = 0;
-	if (where == SEEK_CUR) pos += rz->out;
-	else if (where == SEEK_END) pos += rz->src_end;
-	if(rz->file_type == FILE_TYPE_PLAIN){
-#ifdef _USE_KNETFILE
-		knet_seek(rz->x.fpr, pos, SEEK_SET);
-        seek_pos = knet_tell(rz->x.fpr);
-#else
-		seek_pos = lseek(rz->filedes, pos, SEEK_SET);
-#endif
-		rz->buf_off = rz->buf_len = 0;
-		rz->out = rz->in = seek_pos;
-		return seek_pos;
-	} else if(rz->file_type == FILE_TYPE_GZ){
-		if(pos >= rz->out) goto SKIP;
-		return rz->out;
-	}
-	if(pos == rz->out) return pos;
-	if(pos > rz->src_end) return rz->out;
-	if(!rz->seekable || !rz->load_index){
-		if(pos >= rz->out) goto SKIP;
-	}
-	idx = pos / RZ_BLOCK_SIZE - 1;
-	seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
-	new_out  = (idx + 1) * RZ_BLOCK_SIZE;
-	if(pos > rz->out && new_out <= rz->out) goto SKIP;
-	_razf_reset_read(rz, seek_pos, new_out);
-	SKIP:
-	razf_skip(rz, (int)(pos - rz->out));
-	return rz->out;
-}
-
-uint64_t razf_tell2(RAZF *rz)
-{
-	/*
-	if (rz->load_index) {
-		int64_t idx, seek_pos;
-		idx = rz->out / RZ_BLOCK_SIZE - 1;
-		seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
-		if (seek_pos != rz->block_pos || rz->out%RZ_BLOCK_SIZE != rz->block_off)
-			fprintf(stderr, "[razf_tell2] inconsistent block offset: (%lld, %lld) != (%lld, %lld)\n",
-					(long long)seek_pos, (long long)rz->out%RZ_BLOCK_SIZE, (long long)rz->block_pos, (long long) rz->block_off);
-	}
-	*/
-	return (uint64_t)rz->block_pos<<16 | (rz->block_off&0xffff);
-}
-
-int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where)
-{
-	if (where != SEEK_SET) return -1;
-	return razf_jump(rz, voffset>>16, voffset&0xffff);
-}
-
-void razf_close(RAZF *rz){
-	if(rz->mode == 'w'){
-#ifndef _RZ_READONLY
-		razf_end_flush(rz);
-		deflateEnd(rz->stream);
-#ifdef _USE_KNETFILE
-		save_zindex(rz, rz->x.fpw);
-		if(is_big_endian()){
-			write(rz->x.fpw, &rz->in, sizeof(int64_t));
-			write(rz->x.fpw, &rz->out, sizeof(int64_t));
-		} else {
-			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
-			write(rz->x.fpw, &v64, sizeof(int64_t));
-			v64 = byte_swap_8((uint64_t)rz->out);
-			write(rz->x.fpw, &v64, sizeof(int64_t));
-		}
-#else
-		save_zindex(rz, rz->filedes);
-		if(is_big_endian()){
-			write(rz->filedes, &rz->in, sizeof(int64_t));
-			write(rz->filedes, &rz->out, sizeof(int64_t));
-		} else {
-			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
-			write(rz->filedes, &v64, sizeof(int64_t));
-			v64 = byte_swap_8((uint64_t)rz->out);
-			write(rz->filedes, &v64, sizeof(int64_t));
-		}
-#endif
-#endif
-	} else if(rz->mode == 'r'){
-		if(rz->stream) inflateEnd(rz->stream);
-	}
-	if(rz->inbuf) free(rz->inbuf);
-	if(rz->outbuf) free(rz->outbuf);
-	if(rz->header){
-		free(rz->header->extra);
-		free(rz->header->name);
-		free(rz->header->comment);
-		free(rz->header);
-	}
-	if(rz->index){
-		free(rz->index->bin_offsets);
-		free(rz->index->cell_offsets);
-		free(rz->index);
-	}
-	free(rz->stream);
-#ifdef _USE_KNETFILE
-    if (rz->mode == 'r')
-        knet_close(rz->x.fpr);
-    if (rz->mode == 'w')
-        close(rz->x.fpw);
-#else
-	close(rz->filedes);
-#endif
-	free(rz);
-}
-
-#endif