-/*
- * 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;
}
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);
+ int fd, 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);
}
// 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
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 &&
int
read_block(BGZF* fp)
{
- byte header[BLOCK_HEADER_LENGTH];
+ bgzf_byte_t header[BLOCK_HEADER_LENGTH];
int size = 0;
#ifdef _USE_KNETFILE
int64_t block_address = knet_tell(fp->x.fpr);
return -1;
}
int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
- byte* compressed_block = (byte*) fp->compressed_block;
+ 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;
#ifdef _USE_KNETFILE
}
int bytes_read = 0;
- byte* output = data;
+ bgzf_byte_t* output = data;
while (bytes_read < length) {
int available = fp->block_length - fp->block_offset;
if (available <= 0) {
break;
}
}
- int copy_length = min(length-bytes_read, available);
- byte* buffer = fp->uncompressed_block;
+ int copy_length = bgzf_min(length-bytes_read, available);
+ bgzf_byte_t* buffer = fp->uncompressed_block;
memcpy(output, buffer + fp->block_offset, copy_length);
fp->block_offset += copy_length;
output += copy_length;
fp->uncompressed_block = malloc(fp->uncompressed_block_size);
}
- const byte* input = data;
+ const bgzf_byte_t* input = data;
int block_length = fp->uncompressed_block_size;
int 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;
if (flush_block(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 (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)
{
fp->block_offset = block_offset;
return 0;
}
-