* or functionality.
*/
-/* 2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */
+/*
+ 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 <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)
+
+#ifdef _NO_LFS
+#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->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;
}
// 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 &&
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);
+}
+
static
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);
+ if (load_block_from_cache(fp, block_address)) return 0;
int 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);
#endif
if (count == 0) {
fp->block_length = 0;
return 0;
}
+ size = count;
if (count != sizeof(header)) {
report_error(fp, "read failed");
return -1;
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
report_error(fp, "read failed");
return -1;
}
+ size += count;
count = inflate_block(fp, block_length);
if (count < 0) {
return -1;
}
fp->block_address = block_address;
fp->block_length = count;
+ cache_block(fp, size);
return 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;
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
}
free(fp->uncompressed_block);
free(fp->compressed_block);
+ free_cache(fp);
free(fp);
return 0;
}
return ((fp->block_address << 16) | (fp->block_offset & 0xFFFF));
}
+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)
{
fp->block_offset = block_offset;
return 0;
}
-
projects / samtools.git / blobdiff