-/*
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2008 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever.
- * Neither the Broad Institute nor MIT can be responsible for its use, misuse,
- * or functionality.
- */
+/* 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.
} 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 byte;
+typedef int8_t bgzf_byte_t;
static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
static const int MAX_BLOCK_SIZE = 64 * 1024;
buffer[3] = value >> 24;
}
-inline
+static inline
int
-min(int x, int y)
+bgzf_min(int x, int y)
{
return (x < y) ? x : y;
}
static
BGZF*
-open_write(int fd, bool is_uncompressed)
+open_write(int fd, int compress_level) // compress_level==-1 for the default level
{
FILE* file = fdopen(fd, "w");
BGZF* fp;
fp = malloc(sizeof(BGZF));
fp->file_descriptor = fd;
fp->open_mode = 'w';
- fp->owned_file = 0; fp->is_uncompressed = is_uncompressed;
+ 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
bgzf_open(const char* __restrict path, const char* __restrict mode)
{
BGZF* fp = NULL;
- if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
+ 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->open_mode = 'r';
fp->x.fpr = file;
#else
- int oflag = O_RDONLY;
- int fd = open(path, oflag);
+ 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 (mode[0] == 'w' || mode[0] == 'W') {
- int oflag = O_WRONLY | O_CREAT | O_TRUNC;
- int fd = open(path, oflag, 0644);
+ } 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;
- fp = open_write(fd, strstr(mode, "u")? 1 : 0);
- }
- if (fp != NULL) {
- fp->owned_file = 1;
+ { // 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;
}
if (mode[0] == 'r' || mode[0] == 'R') {
return open_read(fd);
} else if (mode[0] == 'w' || mode[0] == 'W') {
- return open_write(fd, strstr(mode, "u")? 1 : 0);
+ 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;
}
// Deflate the block in fp->uncompressed_block into fp->compressed_block.
// Also adds an extra field that stores the compressed block length.
- byte* buffer = fp->compressed_block;
+ bgzf_byte_t* buffer = fp->compressed_block;
int buffer_size = fp->compressed_block_size;
// Init gzip header
int input_length = block_length;
int compressed_length = 0;
while (1) {
- int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION;
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
- int status = deflateInit2(&zs, compress_level, Z_DEFLATED,
+ 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");
// 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.next_out = fp->uncompressed_block;
zs.avail_out = fp->uncompressed_block_size;
- int status = inflateInit2(&zs, GZIP_WINDOW_BITS);
+ status = inflateInit2(&zs, GZIP_WINDOW_BITS);
if (status != Z_OK) {
report_error(fp, "inflate init failed");
return -1;
static
int
-check_header(const byte* header)
+check_header(const bgzf_byte_t* header)
{
return (header[0] == GZIP_ID1 &&
- header[1] == (byte) GZIP_ID2 &&
+ header[1] == (bgzf_byte_t) GZIP_ID2 &&
header[2] == Z_DEFLATED &&
(header[3] & FLG_FEXTRA) != 0 &&
unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
}
-static
int
-read_block(BGZF* fp)
+bgzf_read_block(BGZF* fp)
{
- byte header[BLOCK_HEADER_LENGTH];
- int size = 0;
+ 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;
- int count = knet_read(fp->x.fpr, header, sizeof(header));
+ 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;
- int count = fread(header, 1, sizeof(header), fp->file);
+ count = fread(header, 1, sizeof(header), fp->file);
#endif
if (count == 0) {
fp->block_length = 0;
report_error(fp, "invalid block header");
return -1;
}
- int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
- byte* compressed_block = (byte*) fp->compressed_block;
+ 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);
- int remaining = block_length - 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
}
size += count;
count = inflate_block(fp, block_length);
- if (count < 0) {
- return -1;
- }
+ if (count < 0) return -1;
if (fp->block_length != 0) {
// Do not reset offset if this read follows a seek.
fp->block_offset = 0;
}
int bytes_read = 0;
- byte* output = data;
+ bgzf_byte_t* output = data;
while (bytes_read < length) {
- int available = fp->block_length - fp->block_offset;
+ int copy_length, available = fp->block_length - fp->block_offset;
+ bgzf_byte_t *buffer;
if (available <= 0) {
- if (read_block(fp) != 0) {
+ if (bgzf_read_block(fp) != 0) {
return -1;
}
available = fp->block_length - fp->block_offset;
break;
}
}
- int copy_length = min(length-bytes_read, available);
- byte* buffer = fp->uncompressed_block;
+ 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;
return bytes_read;
}
-static
-int
-flush_block(BGZF* fp)
+int bgzf_flush(BGZF* fp)
{
while (fp->block_offset > 0) {
- int block_length = deflate_block(fp, fp->block_offset);
- if (block_length < 0) {
- return -1;
- }
+ int count, block_length;
+ block_length = deflate_block(fp, fp->block_offset);
+ if (block_length < 0) return -1;
#ifdef _USE_KNETFILE
- int count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+ count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
#else
- int count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+ count = fwrite(fp->compressed_block, 1, block_length, fp->file);
#endif
if (count != block_length) {
report_error(fp, "write failed");
return 0;
}
-int
-bgzf_write(BGZF* fp, const void* data, int length)
+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) {
+ if (fp->uncompressed_block == NULL)
fp->uncompressed_block = malloc(fp->uncompressed_block_size);
- }
- const byte* input = data;
- int block_length = fp->uncompressed_block_size;
- int bytes_written = 0;
+ input = data;
+ block_length = fp->uncompressed_block_size;
+ bytes_written = 0;
while (bytes_written < length) {
- int copy_length = min(block_length - fp->block_offset, length - bytes_written);
- byte* buffer = fp->uncompressed_block;
+ 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 (flush_block(fp) != 0) {
+ if (bgzf_flush(fp) != 0) {
break;
}
}
return bytes_written;
}
-int
-bgzf_close(BGZF* fp)
+int bgzf_close(BGZF* fp)
{
if (fp->open_mode == 'w') {
- if (flush_block(fp) != 0) {
- return -1;
- }
+ 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
else ret = knet_close(fp->x.fpr);
if (ret != 0) return -1;
#else
- if (fclose(fp->file) != 0) {
- return -1;
- }
+ if (fclose(fp->file) != 0) return -1;
#endif
}
free(fp->uncompressed_block);
return 0;
}
-int64_t
-bgzf_tell(BGZF* fp)
+void bgzf_set_cache_size(BGZF *fp, int cache_size)
{
- return ((fp->block_address << 16) | (fp->block_offset & 0xFFFF));
+ if (fp) fp->cache_size = cache_size;
}
-void bgzf_set_cache_size(BGZF *fp, int cache_size)
+int bgzf_check_EOF(BGZF *fp)
{
- if (fp) fp->cache_size = cache_size;
+ 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)
+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;
report_error(fp, "unimplemented seek option");
return -1;
}
- int block_offset = pos & 0xFFFF;
- int64_t block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
+ block_offset = pos & 0xFFFF;
+ block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
#ifdef _USE_KNETFILE
if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
#else
fp->block_offset = block_offset;
return 0;
}
-
projects / samtools.git / blobdiff