bgzf.c

/* The MIT License
 
 Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
 2011 Attractive Chaos <attractor@live.co.uk>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
 in the Software without restriction, including without limitation the rights
 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
 The above copyright notice and this permission notice shall be included in
 all copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 */

/*
 2009-06-29 by lh3: cache recent uncompressed blocks.
 2009-06-25 by lh3: optionally use my knetfile library to access file on a FTP.
 2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <assert.h>
#include <fcntl.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "bgzf.h"

#ifdef BGZF_CACHE
#include "khash.h"
typedef struct {
	int size;
	uint8_t *block;
	int64_t end_offset;
} cache_t;
KHASH_MAP_INIT_INT64(cache, cache_t)
#endif

#if defined(_WIN32) || defined(_MSC_VER)
#define ftello(fp) ftell(fp)
#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
#else
extern off_t ftello(FILE *stream);
extern int fseeko(FILE *stream, off_t offset, int whence);
#endif

typedef FILE *_bgzf_file_t;
#define _bgzf_open(fn, mode) fopen(fn, mode)
#define _bgzf_dopen(fp, mode) fdopen(fp, mode)
#define _bgzf_close(fp) fclose(fp)
#define _bgzf_fileno(fp) fileno(fp)
#define _bgzf_tell(fp) ftello(fp)
#define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence)
#define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp)
#define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp)

typedef int8_t bgzf_byte_t;
static const int DEFAULT_BLOCK_SIZE  = 64 * 1024;
static const int MAX_BLOCK_SIZE      = 64 * 1024;
static const int BLOCK_HEADER_LENGTH = 18;
static const int BLOCK_FOOTER_LENGTH = 8;
static const int GZIP_ID1            = 31;
static const int GZIP_ID2            = 139;
static const int CM_DEFLATE          = 8;
static const int FLG_FEXTRA          = 4;
static const int OS_UNKNOWN          = 255;
static const int BGZF_ID1            = 66; // 'B'
static const int BGZF_ID2            = 67; // 'C'
static const int BGZF_LEN            = 2;
static const int BGZF_XLEN           = 6; // BGZF_LEN+4
static const int GZIP_WINDOW_BITS    = -15; // no zlib header
static const int Z_DEFAULT_MEM_LEVEL = 8;

/* BGZF/GZIP header (speciallized from RFC 1952; little endian):
 +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
 | 31|139|  8|  4|              0|  0|255|      6| 66| 67|      2|BLK_LEN|
 +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
 */
static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0";

static inline void packInt16(uint8_t *buffer, uint16_t value)
{
	buffer[0] = value;
	buffer[1] = value >> 8;
}

static inline int unpackInt16(const uint8_t *buffer)
{
	return (buffer[0] | (buffer[1] << 8));
}

static inline void packInt32(uint8_t *buffer, uint32_t value)
{
	buffer[0] = value;
	buffer[1] = value >> 8;
	buffer[2] = value >> 16;
	buffer[3] = value >> 24;
}

static inline int bgzf_min(int x, int y)
{
	return (x < y) ? x : y;
}

static void report_error(BGZF* fp, const char* message)
{
	fp->error = message;
}

static BGZF *bgzf_read_init()
{
	BGZF *fp;
	fp = (BGZF*)calloc(1, sizeof(BGZF));
	fp->open_mode = 'r';
	fp->uncompressed_block_size = MAX_BLOCK_SIZE;
	fp->uncompressed_block      = malloc(MAX_BLOCK_SIZE);
	fp->compressed_block_size   = MAX_BLOCK_SIZE;
	fp->compressed_block        = malloc(MAX_BLOCK_SIZE);
	fp->cache_size = 0;
#ifdef BGZF_CACHE
	fp->cache = kh_init(cache);
#endif
	return fp;
}

static BGZF* open_read(int fd)
{
	//#ifdef _USE_KNETFILE
	//    knetFile *file = knet_dopen(fd, "r");
	//#else
	FILE* file = fdopen(fd, "r");
	//#endif
	BGZF* fp;
	if (file == 0) return 0;
	fp = bgzf_read_init();
	fp->file_descriptor = fd;
	fp->open_mode = 'r';
	//#ifdef _USE_KNETFILE
	//    fp->x.fpr = file;
	//#else
	fp->file = file;
	//#endif
	return fp;
}

static BGZF* open_write(int fd, int compress_level) // compress_level==-1 for the default level
{
	FILE* file = fdopen(fd, "w");
	BGZF* fp;
	if (file == 0) return 0;
	fp = (BGZF*)malloc(sizeof(BGZF));
	fp->file_descriptor = fd;
	fp->open_mode = 'w';
	fp->owned_file = 0;
	fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
	if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
	//#ifdef _USE_KNETFILE
	//    fp->x.fpw = file;
	//#else
	fp->file = file;
	//#endif
	fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
	fp->uncompressed_block = NULL;
	fp->compressed_block_size = MAX_BLOCK_SIZE;
	fp->compressed_block = malloc(MAX_BLOCK_SIZE);
	fp->block_address = 0;
	fp->block_offset = 0;
	fp->block_length = 0;
	fp->error = NULL;
	return fp;
}

static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level
{
	BGZF *fp;
	fp = (BGZF*)calloc(1, sizeof(BGZF));
	fp->open_mode = 'w';
	fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE);
	fp->compressed_block = malloc(BGZF_BLOCK_SIZE);
	fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
	if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
	return fp;
}

// get the compress level from the mode string
static int mode2level(const char *__restrict mode)
{
	int i, compress_level = -1;
	for (i = 0; mode[i]; ++i)
		if (mode[i] >= '0' && mode[i] <= '9') break;
	if (mode[i]) compress_level = (int)mode[i] - '0';
	if (strchr(mode, 'u')) compress_level = 0;
	return compress_level;
}

BGZF* bgzf_open(const char* __restrict path, const char* __restrict mode)
{
	BGZF* fp = NULL;
	if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
		int fd, oflag = O_RDONLY;
#ifdef _WIN32
		oflag |= O_BINARY;
#endif
		fd = open(path, oflag);
		if (fd == -1) return 0;
		fp = open_read(fd);
	} else if (strchr(mode, 'w') || strchr(mode, 'W')) {
		int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
#ifdef _WIN32
		oflag |= O_BINARY;
#endif
		fd = open(path, oflag, 0666);
		if (fd == -1) return 0;
		{ // set compress_level
			int i;
			for (i = 0; mode[i]; ++i)
				if (mode[i] >= '0' && mode[i] <= '9') break;
			if (mode[i]) compress_level = (int)mode[i] - '0';
			if (strchr(mode, 'u')) compress_level = 0;
		}
		fp = open_write(fd, compress_level);
	}
	if (fp != NULL) fp->owned_file = 1;
	return fp;
}

BGZF *bgzf_dopen(int fd, const char *mode)
{
	BGZF *fp = 0;
	if (strchr(mode, 'r') || strchr(mode, 'R')) {
		_bgzf_file_t fpr;
		if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0;
		fp = bgzf_read_init();
		fp->file= fpr;
	} else if (strchr(mode, 'w') || strchr(mode, 'W')) {
		FILE *fpw;
		if ((fpw = fdopen(fd, "w")) == 0) return 0;
		fp = bgzf_write_init(mode2level(mode));
		fp->file = fpw;
	}
	return fp;
}

BGZF* bgzf_fdopen(int fd, const char * __restrict mode)
{
	if (fd == -1) return 0;
	if (mode[0] == 'r' || mode[0] == 'R') {
		return open_read(fd);
	} else if (mode[0] == 'w' || mode[0] == 'W') {
		int i, compress_level = -1;
		for (i = 0; mode[i]; ++i)
			if (mode[i] >= '0' && mode[i] <= '9') break;
		if (mode[i]) compress_level = (int)mode[i] - '0';
		if (strchr(mode, 'u')) compress_level = 0;
		return open_write(fd, compress_level);
	} else {
		return NULL;
	}
}

static int deflate_block(BGZF* fp, int block_length)
{
	// Deflate the block in fp->uncompressed_block into fp->compressed_block.
	// Also adds an extra field that stores the compressed block length.
	
	bgzf_byte_t* buffer = (bgzf_byte_t*)(fp->compressed_block);
	int buffer_size = fp->compressed_block_size;
	
	// Init gzip header
	buffer[0] = GZIP_ID1;
	buffer[1] = GZIP_ID2;
	buffer[2] = CM_DEFLATE;
	buffer[3] = FLG_FEXTRA;
	buffer[4] = 0; // mtime
	buffer[5] = 0;
	buffer[6] = 0;
	buffer[7] = 0;
	buffer[8] = 0;
	buffer[9] = OS_UNKNOWN;
	buffer[10] = BGZF_XLEN;
	buffer[11] = 0;
	buffer[12] = BGZF_ID1;
	buffer[13] = BGZF_ID2;
	buffer[14] = BGZF_LEN;
	buffer[15] = 0;
	buffer[16] = 0; // placeholder for block length
	buffer[17] = 0;
	
	// loop to retry for blocks that do not compress enough
	int input_length = block_length;
	int compressed_length = 0;
	while (1) {
		z_stream zs;
		zs.zalloc    = NULL;
		zs.zfree     = NULL;
		zs.next_in   = (Bytef*)(fp->uncompressed_block);
		zs.avail_in  = input_length;
		zs.next_out  = (Bytef*)&buffer[BLOCK_HEADER_LENGTH];
		zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
		
		int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED, GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
		if (status != Z_OK) {
			report_error(fp, "deflate init failed");
			return -1;
		}
		status = deflate(&zs, Z_FINISH);
		if (status != Z_STREAM_END) {
			deflateEnd(&zs);
			if (status == Z_OK) {
				// Not enough space in buffer.
				// Can happen in the rare case the input doesn't compress enough.
				// Reduce the amount of input until it fits.
				input_length -= 1024;
				if (input_length <= 0) {
					// should never happen
					report_error(fp, "input reduction failed");
					return -1;
				}
				continue;
			}
			report_error(fp, "deflate failed");
			return -1;
		}
		status = deflateEnd(&zs);
		if (status != Z_OK) {
			report_error(fp, "deflate end failed");
			return -1;
		}
		compressed_length = zs.total_out;
		compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
		if (compressed_length > MAX_BLOCK_SIZE) {
			// should never happen
			report_error(fp, "deflate overflow");
			return -1;
		}
		break;
	}
	
	packInt16((uint8_t*)&buffer[16], compressed_length-1);
	uint32_t crc = crc32(0L, NULL, 0L);
	crc = crc32(crc, (const Bytef*)(fp->uncompressed_block), input_length);
	packInt32((uint8_t*)&buffer[compressed_length-8], crc);
	packInt32((uint8_t*)&buffer[compressed_length-4], input_length);
	
	int remaining = block_length - input_length;
	if (remaining > 0) {
		if (remaining > input_length) {
			// should never happen (check so we can use memcpy)
			report_error(fp, "remainder too large");
			return -1;
		}
		memcpy(fp->uncompressed_block, (Bytef*)(fp->uncompressed_block) + input_length, remaining);
	}
	fp->block_offset = remaining;
	return compressed_length;
}

static int inflate_block(BGZF* fp, int block_length)
{
	// Inflate the block in fp->compressed_block into fp->uncompressed_block
	
	z_stream zs;
	int status;
	zs.zalloc    = NULL;
	zs.zfree     = NULL;
	zs.next_in   = (Bytef*)(fp->compressed_block) + 18;
	zs.avail_in  = block_length - 16;
	zs.next_out  = (Bytef*)(fp->uncompressed_block);
	zs.avail_out = fp->uncompressed_block_size;
	
	status = inflateInit2(&zs, GZIP_WINDOW_BITS);
	if (status != Z_OK) {
		report_error(fp, "inflate init failed");
		return -1;
	}
	status = inflate(&zs, Z_FINISH);
	if (status != Z_STREAM_END) {
		inflateEnd(&zs);
		report_error(fp, "inflate failed");
		return -1;
	}
	status = inflateEnd(&zs);
	if (status != Z_OK) {
		report_error(fp, "inflate failed");
		return -1;
	}
	return zs.total_out;
}

static int check_header(const bgzf_byte_t* header)
{
	return (header[0] == GZIP_ID1 &&
			header[1] == (bgzf_byte_t) GZIP_ID2 &&
			header[2] == Z_DEFLATED &&
			(header[3] & FLG_FEXTRA) != 0 &&
			unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
			header[12] == BGZF_ID1 &&
			header[13] == BGZF_ID2 &&
			unpackInt16((uint8_t*)&header[14]) == BGZF_LEN);
}

#ifdef BGZF_CACHE
static void free_cache(BGZF *fp)
{
	khint_t k;
	khash_t(cache) *h = (khash_t(cache)*)fp->cache;
	if (fp->open_mode != 'r') return;
	for (k = kh_begin(h); k < kh_end(h); ++k)
		if (kh_exist(h, k)) free(kh_val(h, k).block);
	kh_destroy(cache, h);
}

static int load_block_from_cache(BGZF *fp, int64_t block_address)
{
	khint_t k;
	cache_t *p;
	khash_t(cache) *h = (khash_t(cache)*)fp->cache;
	k = kh_get(cache, h, block_address);
	if (k == kh_end(h)) return 0;
	p = &kh_val(h, k);
	if (fp->block_length != 0) fp->block_offset = 0;
	fp->block_address = block_address;
	fp->block_length = p->size;
	memcpy(fp->uncompressed_block, p->block, MAX_BLOCK_SIZE);
	//#ifdef _USE_KNETFILE
	//	knet_seek(fp->x.fpr, p->end_offset, SEEK_SET);
	//#else
	fseeko(fp->file, p->end_offset, SEEK_SET);
	//#endif
	return p->size;
}

static void cache_block(BGZF *fp, int size)
{
	int ret;
	khint_t k;
	cache_t *p;
	khash_t(cache) *h = (khash_t(cache)*)fp->cache;
	if (MAX_BLOCK_SIZE >= fp->cache_size) return;
	if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) {
		/* A better way would be to remove the oldest block in the
		 * cache, but here we remove a random one for simplicity. This
		 * should not have a big impact on performance. */
		for (k = kh_begin(h); k < kh_end(h); ++k)
			if (kh_exist(h, k)) break;
		if (k < kh_end(h)) {
			free(kh_val(h, k).block);
			kh_del(cache, h, k);
		}
	}
	k = kh_put(cache, h, fp->block_address, &ret);
	if (ret == 0) return; // if this happens, a bug!
	p = &kh_val(h, k);
	p->size = fp->block_length;
	p->end_offset = fp->block_address + size;
	p->block = (uint8_t*)malloc(MAX_BLOCK_SIZE);
	memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
}
#else
static void free_cache(BGZF *fp) {}
static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;}
static void cache_block(BGZF *fp, int size) {}
#endif

int bgzf_read_block(BGZF* fp)
{
	bgzf_byte_t header[BLOCK_HEADER_LENGTH];
	int count, size = 0, block_length, remaining;
	//#ifdef _USE_KNETFILE
	//    int64_t block_address = knet_tell(fp->x.fpr);
	//	if (load_block_from_cache(fp, block_address)) return 0;
	//    count = knet_read(fp->x.fpr, header, sizeof(header));
	//#else
	int64_t block_address = ftello(fp->file);
	if (load_block_from_cache(fp, block_address)) return 0;
	count = fread(header, 1, sizeof(header), fp->file);
	//#endif
	if (count == 0) {
		fp->block_length = 0;
		return 0;
	}
	size = count;
	if (count != sizeof(header)) {
		report_error(fp, "read failed");
		return -1;
	}
	if (!check_header(header)) {
		report_error(fp, "invalid block header");
		return -1;
	}
	block_length = unpackInt16((uint8_t*)&header[16]) + 1;
	bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
	memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
	remaining = block_length - BLOCK_HEADER_LENGTH;
	//#ifdef _USE_KNETFILE
	//    count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
	//#else
	count = fread(&compressed_block[BLOCK_HEADER_LENGTH], 1, remaining, fp->file);
	//#endif
	if (count != remaining) {
		report_error(fp, "read failed");
		return -1;
	}
	size += count;
	count = inflate_block(fp, block_length);
	if (count < 0) return -1;
	if (fp->block_length != 0) {
		// Do not reset offset if this read follows a seek.
		fp->block_offset = 0;
	}
	fp->block_address = block_address;
	fp->block_length = count;
	cache_block(fp, size);
	return 0;
}

int bgzf_read(BGZF* fp, void* data, int length)
{
	if (length <= 0) {
		return 0;
	}
	if (fp->open_mode != 'r') {
		report_error(fp, "file not open for reading");
		return -1;
	}
	
	int bytes_read = 0;
	bgzf_byte_t* output = (bgzf_byte_t*)data;
	while (bytes_read < length) {
		int copy_length, available = fp->block_length - fp->block_offset;
		bgzf_byte_t *buffer;
		if (available <= 0) {
			if (bgzf_read_block(fp) != 0) {
				return -1;
			}
			available = fp->block_length - fp->block_offset;
			if (available <= 0) {
				break;
			}
		}
		copy_length = bgzf_min(length-bytes_read, available);
		buffer = (bgzf_byte_t*)(fp->uncompressed_block);
		memcpy(output, buffer + fp->block_offset, copy_length);
		fp->block_offset += copy_length;
		output += copy_length;
		bytes_read += copy_length;
	}
	if (fp->block_offset == fp->block_length) {
		//#ifdef _USE_KNETFILE
		//        fp->block_address = knet_tell(fp->x.fpr);
		//#else
		fp->block_address = ftello(fp->file);
		//#endif
		fp->block_offset = 0;
		fp->block_length = 0;
	}
	return bytes_read;
}

int bgzf_flush(BGZF* fp)
{
	while (fp->block_offset > 0) {
		int count, block_length;
		block_length = deflate_block(fp, fp->block_offset);
		if (block_length < 0) return -1;
		//#ifdef _USE_KNETFILE
		//        count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
		//#else
		count = fwrite(fp->compressed_block, 1, block_length, fp->file);
		//#endif
		if (count != block_length) {
			report_error(fp, "write failed");
			return -1;
		}
		fp->block_address += block_length;
	}
	return 0;
}

int bgzf_flush_try(BGZF *fp, int size)
{
	if (fp->block_offset + size > fp->uncompressed_block_size)
		return bgzf_flush(fp);
	return -1;
}

int bgzf_write(BGZF* fp, const void* data, int length)
{
	const bgzf_byte_t *input = (const bgzf_byte_t*)data;
	int block_length, bytes_written;
	if (fp->open_mode != 'w') {
		report_error(fp, "file not open for writing");
		return -1;
	}
	
	if (fp->uncompressed_block == NULL)
		fp->uncompressed_block = malloc(fp->uncompressed_block_size);
	
	input = (const bgzf_byte_t*)data;
	block_length = fp->uncompressed_block_size;
	bytes_written = 0;
	while (bytes_written < length) {
		int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
		bgzf_byte_t* buffer = (bgzf_byte_t*)(fp->uncompressed_block);
		memcpy(buffer + fp->block_offset, input, copy_length);
		fp->block_offset += copy_length;
		input += copy_length;
		bytes_written += copy_length;
		if (fp->block_offset == block_length) {
			if (bgzf_flush(fp) != 0) {
				break;
			}
		}
	}
	return bytes_written;
}

int bgzf_close(BGZF* fp)
{
	if (fp->open_mode == 'w') {
		if (bgzf_flush(fp) != 0) return -1;
		{ // add an empty block
			int count, block_length = deflate_block(fp, 0);
			//#ifdef _USE_KNETFILE
			//			count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
			//#else
			count = fwrite(fp->compressed_block, 1, block_length, fp->file);
			//#endif
		}
		//#ifdef _USE_KNETFILE
		//        if (fflush(fp->x.fpw) != 0) {
		//#else
		if (fflush(fp->file) != 0) {
			//#endif
			report_error(fp, "flush failed");
			return -1;
		}
	}
	if (fp->owned_file) {
		//#ifdef _USE_KNETFILE
		//		int ret;
		//		if (fp->open_mode == 'w') ret = fclose(fp->x.fpw);
		//		else ret = knet_close(fp->x.fpr);
		//        if (ret != 0) return -1;
		//#else
		if (fclose(fp->file) != 0) return -1;
		//#endif
	}
	free(fp->uncompressed_block);
	free(fp->compressed_block);
	free_cache(fp);
	free(fp);
	return 0;
}

void bgzf_set_cache_size(BGZF *fp, int cache_size)
{
	if (fp) fp->cache_size = cache_size;
}

int bgzf_check_EOF(BGZF *fp)
{
	static uint8_t magic[29] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
	uint8_t buf[28];
	off_t offset;
	//#ifdef _USE_KNETFILE
	//	offset = knet_tell(fp->x.fpr);
	//	if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
	//	knet_read(fp->x.fpr, buf, 28);
	//	knet_seek(fp->x.fpr, offset, SEEK_SET);
	//#else
	offset = ftello(fp->file);
	if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
	fread(buf, 1, 28, fp->file);
	fseeko(fp->file, offset, SEEK_SET);
	//#endif
	return (memcmp(magic, buf, 28) == 0)? 1 : 0;
}

int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
{
	int block_offset;
	int64_t block_address;
	
	if (fp->open_mode != 'r') {
		report_error(fp, "file not open for read");
		return -1;
	}
	if (where != SEEK_SET) {
		report_error(fp, "unimplemented seek option");
		return -1;
	}
	block_offset = pos & 0xFFFF;
	block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
	//#ifdef _USE_KNETFILE
	//    if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
	//#else
	if (fseeko(fp->file, block_address, SEEK_SET) != 0) {
		//#endif
		report_error(fp, "seek failed");
		return -1;
	}
	fp->block_length = 0;  // indicates current block is not loaded
	fp->block_address = block_address;
	fp->block_offset = block_offset;
	return 0;
}

int bgzf_is_bgzf(const char *fn)
{
	uint8_t buf[16];
	int n;
	_bgzf_file_t fp;
	if ((fp = _bgzf_open(fn, "r")) == 0) return 0;
	n = _bgzf_read(fp, buf, 16);
	_bgzf_close(fp);
	if (n != 16) return 0;
	return memcmp(g_magic, buf, 16) == 0? 1 : 0;
}

int bgzf_check_bgzf(const char *fn)
{
	BGZF *fp;
	uint8_t buf[10],magic[11]="\037\213\010\4\0\0\0\0\0\377";
	int n;
	
	if ((fp = bgzf_open(fn, "r")) == 0)
	{
		fprintf(stderr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
		return -1;
	}
	
	//#ifdef _USE_KNETFILE
	//    n = knet_read(fp->x.fpr, buf, 10);
	//#else
	n = fread(buf, 1, 10, fp->file);
	//#endif
	bgzf_close(fp);
	
	if ( n!=10 )
		return -1;
	
	if ( !memcmp(magic, buf, 10) ) return 1;
	return 0;
}

int bgzf_getc(BGZF *fp)
{
	int c;
	if (fp->block_offset >= fp->block_length) {
		if (bgzf_read_block(fp) != 0) return -2; /* error */
		if (fp->block_length == 0) return -1; /* end-of-file */
	}
	c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
	if (fp->block_offset == fp->block_length) {
		fp->block_address = ftello(fp->file);
		fp->block_offset = 0;
		fp->block_length = 0;
	}
	return c;
}

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
{
	int l, state = 0;
	unsigned char *buf = (unsigned char*)fp->uncompressed_block;
	str->l = 0;
	do {
		if (fp->block_offset >= fp->block_length) {
			if (bgzf_read_block(fp) != 0) { state = -2; break; }
			if (fp->block_length == 0) { state = -1; break; }
		}
		for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l);
		if (l < fp->block_length) state = 1;
		l -= fp->block_offset;
		if (str->l + l + 1 >= str->m) {
			str->m = str->l + l + 2;
			kroundup32(str->m);
			str->s = (char*)realloc(str->s, str->m);
		}
		memcpy(str->s + str->l, buf + fp->block_offset, l);
		str->l += l;
		fp->block_offset += l + 1;
		if (fp->block_offset >= fp->block_length) {
			fp->block_address = _bgzf_tell((_bgzf_file_t)fp->file);
			fp->block_offset = 0;
			fp->block_length = 0;
		} 
	} while (state == 0);
	if (str->l == 0 && state < 0) return state;
	str->s[str->l] = 0;
	return str->l;
}