X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Frazf.c.pysam.c;fp=samtools%2Frazf.c.pysam.c;h=40216370559b073fae7a2a15efd0bac3371b797f;hp=0000000000000000000000000000000000000000;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/razf.c.pysam.c b/samtools/razf.c.pysam.c
new file mode 100644
index 0000000..4021637
--- /dev/null
+++ b/samtools/razf.c.pysam.c
@@ -0,0 +1,855 @@
+#include "pysam.h"
+
+/*
+ * 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(pysamerr, "[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(pysamerr, " -- 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(pysamerr,"[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(pysamerr,"[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(pysamerr, "[_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(pysamerr, "[_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(pysamerr, "[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