X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bgzf.c;h=db970c83f621bac471457bc58821e69e186e03ee;hp=66d6b024f5441f694faf1d875febe9fe8e3c248c;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=62781a2daa24d74a3c590e2669fad1fa7cabf933 diff --git a/bgzf.c b/bgzf.c index 66d6b02..db970c8 100644 --- a/bgzf.c +++ b/bgzf.c @@ -148,7 +148,7 @@ open_read(int fd) 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; @@ -156,7 +156,9 @@ open_write(int fd, bool is_uncompressed) 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 @@ -195,13 +197,20 @@ bgzf_open(const char* __restrict path, const char* __restrict mode) fp = open_read(fd); #endif } else if (strchr(mode, 'w') || strchr(mode, 'W')) { - int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC; + 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, strchr(mode, 'u')? 1 : 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; @@ -214,7 +223,12 @@ bgzf_fdopen(int fd, const char * __restrict mode) 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; } @@ -254,7 +268,6 @@ deflate_block(BGZF* fp, int block_length) 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; @@ -263,7 +276,7 @@ deflate_block(BGZF* fp, int block_length) 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"); @@ -330,6 +343,7 @@ 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; @@ -337,7 +351,7 @@ inflate_block(BGZF* fp, int block_length) 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; @@ -431,7 +445,7 @@ int bgzf_read_block(BGZF* fp) { bgzf_byte_t header[BLOCK_HEADER_LENGTH]; - int count, size = 0; + 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; @@ -454,10 +468,10 @@ bgzf_read_block(BGZF* fp) report_error(fp, "invalid block header"); return -1; } - int block_length = unpackInt16((uint8_t*)&header[16]) + 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); - 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 @@ -494,7 +508,8 @@ bgzf_read(BGZF* fp, void* data, int length) int bytes_read = 0; 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 (bgzf_read_block(fp) != 0) { return -1; @@ -504,8 +519,8 @@ bgzf_read(BGZF* fp, void* data, int length) break; } } - int copy_length = bgzf_min(length-bytes_read, available); - bgzf_byte_t* 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; @@ -552,6 +567,8 @@ int bgzf_flush_try(BGZF *fp, int size) 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; @@ -560,9 +577,9 @@ int bgzf_write(BGZF* fp, const void* data, int length) if (fp->uncompressed_block == NULL) fp->uncompressed_block = malloc(fp->uncompressed_block_size); - const bgzf_byte_t* 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 = bgzf_min(block_length - fp->block_offset, length - bytes_written); bgzf_byte_t* buffer = fp->uncompressed_block;