* samtools-0.1.4-18 (r363)

[samtools.git] / bgzf.c

diff --git a/bgzf.c b/bgzf.c
index c49215c0ed5ac11e9e1f242f397860e7e21c35e8..fe4e31da109f6ca523e73088fb3fd27aa9672587 100644 (file)
--- a/bgzf.c
+++ b/bgzf.c
@@ -10,6 +10,7 @@
  */
 
 /*
+  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 */
 
@@ -22,6 +23,14 @@
 #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)
+
 extern off_t ftello(FILE *stream);
 extern int fseeko(FILE *stream, off_t offset, int whence);
 
@@ -93,6 +102,8 @@ static BGZF *bgzf_read_init()
     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;
 }
 
@@ -338,22 +349,83 @@ check_header(const byte* header)
             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];
+       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;
@@ -375,6 +447,7 @@ read_block(BGZF* fp)
         report_error(fp, "read failed");
         return -1;
     }
+       size += count;
     count = inflate_block(fp, block_length);
     if (count < 0) {
         return -1;
@@ -385,6 +458,7 @@ read_block(BGZF* fp)
     }
     fp->block_address = block_address;
     fp->block_length = count;
+       cache_block(fp, size);
     return 0;
 }
 
@@ -515,6 +589,7 @@ bgzf_close(BGZF* fp)
     }
     free(fp->uncompressed_block);
     free(fp->compressed_block);
+       free_cache(fp);
     free(fp);
     return 0;
 }
@@ -525,6 +600,11 @@ bgzf_tell(BGZF* fp)
     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;
+}
+
 int64_t
 bgzf_seek(BGZF* fp, int64_t pos, int where)
 {