diff pyPRADA_1.2/tools/samtools-0.1.16/bgzf.c @ 0:acc2ca1a3ba4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bgzf.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,714 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   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 <fcntl.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include "bgzf.h"
+
+#include "khash.h"
+typedef struct {
+	int size;
+	uint8_t *block;
+	int64_t end_offset;
+} cache_t;
+KHASH_MAP_INIT_INT64(cache, cache_t)
+
+#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 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;
+
+
+inline
+void
+packInt16(uint8_t* buffer, uint16_t value)
+{
+    buffer[0] = value;
+    buffer[1] = value >> 8;
+}
+
+inline
+int
+unpackInt16(const uint8_t* buffer)
+{
+    return (buffer[0] | (buffer[1] << 8));
+}
+
+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;
+}
+
+int bgzf_check_bgzf(const char *fn)
+{
+    BGZF *fp;
+    uint8_t buf[10],magic[10]="\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;
+}
+
+static BGZF *bgzf_read_init()
+{
+	BGZF *fp;
+	fp = calloc(1, sizeof(BGZF));
+    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;
+	fp->cache = kh_init(cache);
+	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 = 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;
+}
+
+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. */
+#ifdef _USE_KNETFILE
+		knetFile *file = knet_open(path, mode);
+		if (file == 0) return 0;
+		fp = bgzf_read_init();
+		fp->file_descriptor = -1;
+		fp->open_mode = 'r';
+		fp->x.fpr = file;
+#else
+		int fd, oflag = O_RDONLY;
+#ifdef _WIN32
+		oflag |= O_BINARY;
+#endif
+		fd = open(path, oflag);
+		if (fd == -1) return 0;
+        fp = open_read(fd);
+#endif
+    } 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_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 = 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 = fp->uncompressed_block;
+        zs.avail_in = input_length;
+        zs.next_out = (void*)&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, 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,
+               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 = fp->compressed_block + 18;
+    zs.avail_in = block_length - 16;
+    zs.next_out = 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);
+}
+
+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 = malloc(MAX_BLOCK_SIZE);
+	memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
+}
+
+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 = 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 = 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 = 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 = 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 = 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[28] = "\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;
+}