htslib.bgzf

Undocumented in source.

Members

Aliases

bgzidx_t alias bgzidx_t = __bgzidx_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
ssize_t alias ssize_t = int: Undocumented in source.
ssize_t alias ssize_t = long: Undocumented in source.

Functions

bgzf_block_write ssize_t bgzf_block_write(BGZF* fp, const(void)* data, size_t length): Write _length_ bytes from _data_ to the file, the index will be used to decide the amount of uncompressed data to be writen to each bgzip block. If no I/O errors occur, the complete _length_ bytes will be written (or queued for writing). @param fp BGZF file handler @param data data array to write @param length size of data to write @return number of bytes written (i.e., _length_); negative on error
bgzf_check_EOF int bgzf_check_EOF(BGZF* fp): Check if the BGZF end-of-file (EOF) marker is present
bgzf_close int bgzf_close(BGZF* fp): Close the BGZF and free all associated resources.
bgzf_compress int bgzf_compress(void* dst, size_t* dlen, const(void)* src, size_t slen, int level): Compress a single BGZF block.
bgzf_compression int bgzf_compression(BGZF* fp): Return the file's compression format
bgzf_dopen BGZF* bgzf_dopen(int fd, const(char)* mode)
bgzf_fdopen BGZF* bgzf_fdopen(int fd, const(char)* mode): Open an existing file descriptor for reading or writing.
bgzf_flush int bgzf_flush(BGZF* fp): Write the data in the buffer to the file.
bgzf_flush_try int bgzf_flush_try(BGZF* fp, ssize_t size): Flush the file if the remaining buffer size is smaller than _size_ @return 0 if flushing succeeded or was not needed; negative on error
bgzf_getc int bgzf_getc(BGZF* fp): Read one byte from a BGZF file. It is faster than bgzf_read() @param fp BGZF file handler @return byte read; -1 on end-of-file or error
bgzf_getline int bgzf_getline(BGZF* fp, int delim, kstring_t* str): Read one line from a BGZF file. It is faster than bgzf_getc()
bgzf_hopen BGZF* bgzf_hopen(hFILE* fp, const(char)* mode): Open an existing hFILE stream for reading or writing.
bgzf_index_build_init int bgzf_index_build_init(BGZF* fp): Tell BGZF to build index while compressing.
bgzf_index_dump int bgzf_index_dump(BGZF* fp, const(char)* bname, const(char)* suffix): @param fp BGZF file handler @param bname base name @param suffix suffix to add to bname (can be NULL) @return 0 on success and -1 on error.
bgzf_index_dump_hfile int bgzf_index_dump_hfile(BGZF* fp, hFILE* idx, const(char)* name): @param fp BGZF file handle @param idx hFILE to write to @param name file name (for error reporting only, can be NULL) @return 0 on success and -1 on error.
bgzf_index_load int bgzf_index_load(BGZF* fp, const(char)* bname, const(char)* suffix): @param fp BGZF file handler @param bname base name @param suffix suffix to add to bname (can be NULL) @return 0 on success and -1 on error.
bgzf_index_load_hfile int bgzf_index_load_hfile(BGZF* fp, hFILE* idx, const(char)* name): @param fp BGZF file handle @param idx hFILE to read from @param name file name (for error reporting only; can be NULL) @return 0 on success and -1 on error.
bgzf_is_bgzf int bgzf_is_bgzf(const(char)* fn): Check if a file is in the BGZF format
bgzf_mt int bgzf_mt(BGZF* fp, int n_threads, int n_sub_blks): Enable multi-threading (only effective when the library was compiled with -DBGZF_MT)
bgzf_open BGZF* bgzf_open(const(char)* path, const(char)* mode): Open the specified file for reading or writing.
bgzf_peek int bgzf_peek(BGZF* fp): Returns the next byte in the file without consuming it. @param fp BGZF file handler @return -1 on EOF, -2 on error, otherwise the unsigned byte value.
bgzf_raw_read ssize_t bgzf_raw_read(BGZF* fp, void* data, size_t length): Read up to _length_ bytes directly from the underlying stream without decompressing. Bypasses BGZF blocking, so must be used with care in specialised circumstances only.
bgzf_raw_write ssize_t bgzf_raw_write(BGZF* fp, const(void)* data, size_t length): Write _length_ bytes directly to the underlying stream without compressing. Bypasses BGZF blocking, so must be used with care in specialised circumstances only.
bgzf_read ssize_t bgzf_read(BGZF* fp, void* data, size_t length): Read up to _length_ bytes from the file storing into _data_.
bgzf_read_block int bgzf_read_block(BGZF* fp): Read the next BGZF block.
bgzf_seek int64_t bgzf_seek(BGZF* fp, int64_t pos, int whence): Set the file to read from the location specified by _pos_.
bgzf_set_cache_size void bgzf_set_cache_size(BGZF* fp, int size): Set the cache size. Only effective when compiled with -DBGZF_CACHE.
bgzf_tell ulong bgzf_tell(BGZF* fp): Return a virtual file pointer to the current location in the file. No interpretation of the value should be made, other than a subsequent call to bgzf_seek can be used to position the file at the same point. Return value is non-negative on success.
bgzf_thread_pool int bgzf_thread_pool(BGZF* fp, hts_tpool* pool, int qsize): Enable multi-threading (when compiled with -DBGZF_MT) via a shared thread pool. This means both encoder and decoder can balance usage across a single pool of worker jobs.
bgzf_useek int bgzf_useek(BGZF* fp, off_t uoffset, int where): Position BGZF at the uncompressed offset
bgzf_utell off_t bgzf_utell(BGZF* fp): Position in uncompressed BGZF
bgzf_write ssize_t bgzf_write(BGZF* fp, const(void)* data, size_t length): Write _length_ bytes from _data_ to the file. If no I/O errors occur, the complete _length_ bytes will be written (or queued for writing).

Structs

BGZF struct BGZF: Block Gzipped File
__bgzidx_t struct __bgzidx_t: BGZF index
bgzf_cache_t struct bgzf_cache_t: bgzf cache
bgzf_mtaux_t struct bgzf_mtaux_t: klib kstring Memory pool for bgzf_job structs, to avoid many malloc/free, see htslib/bgzf.c
hFILE struct hFILE: see hts.d
hts_tpool struct hts_tpool: see thread_pool.d
z_stream_s struct z_stream_s: replaces zlib::z_stream?

Variables

BGZF_BLOCK_SIZE enum int BGZF_BLOCK_SIZE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_ERR_CRC enum int BGZF_ERR_CRC;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_ERR_HEADER enum int BGZF_ERR_HEADER;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_ERR_IO enum int BGZF_ERR_IO;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_ERR_MISUSE enum int BGZF_ERR_MISUSE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_ERR_MT enum int BGZF_ERR_MT;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_ERR_ZLIB enum int BGZF_ERR_ZLIB;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
BGZF_MAX_BLOCK_SIZE enum int BGZF_MAX_BLOCK_SIZE;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

htslib.bgzf

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