#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <unistd.h>
#include <assert.h>
#include <pthread.h>
#include <sys/types.h>
#include <inttypes.h>
#include "htslib/hts.h"
#include "htslib/bgzf.h"
#include "htslib/hfile.h"
#include "htslib/khash.h"

Classes
struct	cache_t

struct	bgzidx1_t

struct	__bgzidx_t

struct	worker_t

struct	bgzf_mtaux_t

Macros
#define	BLOCK_HEADER_LENGTH 18

#define	BLOCK_FOOTER_LENGTH 8

Typedefs
typedef struct bgzf_mtaux_t	mtaux_t

Functions
void	bgzf_index_destroy (BGZF *fp)

int	bgzf_index_add_block (BGZF *fp)

BGZF *	bgzf_open (const char path, const char mode)

BGZF *	bgzf_dopen (int fd, const char *mode)

BGZF *	bgzf_hopen (hFILE hfp, const char mode)

int	bgzf_read_block (BGZF *fp)

ssize_t	bgzf_read (BGZF fp, void data, size_t length)

ssize_t	bgzf_raw_read (BGZF fp, void data, size_t length)

int	bgzf_mt (BGZF *fp, int n_threads, int n_sub_blks)

int	bgzf_flush (BGZF *fp)

int	bgzf_flush_try (BGZF *fp, ssize_t size)

ssize_t	bgzf_write (BGZF fp, const void data, size_t length)

ssize_t	bgzf_raw_write (BGZF fp, const void data, size_t length)

int	bgzf_close (BGZF *fp)

void	bgzf_set_cache_size (BGZF *fp, int cache_size)

int	bgzf_check_EOF (BGZF *fp)

int64_t	bgzf_seek (BGZF *fp, int64_t pos, int where)

int	bgzf_is_bgzf (const char *fn)

int	bgzf_getc (BGZF *fp)

int	bgzf_getline (BGZF fp, int delim, kstring_t str)

int	bgzf_index_build_init (BGZF *fp)

int	bgzf_index_dump (BGZF fp, const char bname, const char *suffix)

int	bgzf_index_load (BGZF fp, const char bname, const char *suffix)

int	bgzf_useek (BGZF *fp, long uoffset, int where)

long	bgzf_utell (BGZF *fp)

Macro Definition Documentation

#define BLOCK_FOOTER_LENGTH 8

Definition at line 42 of file bgzf.c.

#define BLOCK_HEADER_LENGTH 18

Definition at line 41 of file bgzf.c.

Typedef Documentation

typedef struct bgzf_mtaux_t mtaux_t

Function Documentation

int bgzf_check_EOF ( BGZF * fp)

Check if the BGZF end-of-file (EOF) marker is present

Parameters

fp	BGZF file handler opened for reading

Returns: 1 if the EOF marker is present and correct; 2 if it can't be checked, e.g., because fp isn't seekable; 0 if the EOF marker is absent; -1 (with errno set) on error

Definition at line 797 of file bgzf.c.

int bgzf_close ( BGZF * fp)

Close the BGZF and free all associated resources.

Parameters

fp	BGZF file handler

Returns: 0 on success and -1 on error

Definition at line 760 of file bgzf.c.

BGZF* bgzf_dopen	(	int	fd,
		const char *	mode
	)

Open an existing file descriptor for reading or writing.

Parameters

fd	file descriptor
mode	mode matching /[rwa][u0-9]+/: 'r' for reading, 'w' for writing, or 'a' for appending, while a digit specifies the zlib compression level. Note that there is a distinction between 'u' and '0': the first yields plain uncompressed output whereas the latter outputs uncompressed data wrapped in the zlib format.

Returns: BGZF file handler; 0 on error

Definition at line 177 of file bgzf.c.

int bgzf_flush ( BGZF * fp)

Write the data in the buffer to the file.

Definition at line 700 of file bgzf.c.

int bgzf_flush_try	(	BGZF *	fp,
		ssize_t	size
	)

Flush the file if the remaining buffer size is smaller than size

Returns: 0 if flushing succeeded or was not needed; negative on error

Definition at line 726 of file bgzf.c.

int bgzf_getc ( BGZF * fp)

Read one byte from a BGZF file. It is faster than bgzf_read()

Parameters

fp	BGZF file handler

Returns: byte read; -1 on end-of-file or error

Definition at line 843 of file bgzf.c.

int bgzf_getline	(	BGZF *	fp,
		int	delim,
		kstring_t *	str
	)

Read one line from a BGZF file. It is faster than bgzf_getc()

Parameters

fp	BGZF file handler
delim	delimitor
str	string to write to; must be initialized

Returns: length of the string; 0 on end-of-file; negative on error

Definition at line 864 of file bgzf.c.

BGZF* bgzf_hopen	(	struct hFILE *	fp,
		const char *	mode
	)

Open an existing hFILE stream for reading or writing.

Definition at line 199 of file bgzf.c.

int bgzf_index_add_block ( BGZF * fp)

Definition at line 915 of file bgzf.c.

int bgzf_index_build_init ( BGZF * fp)

Tell BGZF to build index while compressing.

Parameters

fp	BGZF file handler; can be opened for reading or writing.

Returns 0 on success and -1 on error.

Definition at line 906 of file bgzf.c.

void bgzf_index_destroy ( BGZF * fp)

Definition at line 897 of file bgzf.c.

int bgzf_index_dump	(	BGZF *	fp,
		const char *	bname,
		const char *	suffix
	)

Save BGZF index

Parameters

fp	BGZF file handler
bname	base name
suffix	suffix to add to bname (can be NULL)

Returns 0 on success and -1 on error.

Definition at line 930 of file bgzf.c.

int bgzf_index_load	(	BGZF *	fp,
		const char *	bname,
		const char *	suffix
	)

Load BGZF index

Parameters

fp	BGZF file handler
bname	base name
suffix	suffix to add to bname (can be NULL)

Returns 0 on success and -1 on error.

Definition at line 980 of file bgzf.c.

int bgzf_is_bgzf ( const char * fn)

Check if a file is in the BGZF format

Parameters

fn file name

Returns: 1 if fn is BGZF; 0 if not or on I/O error

Definition at line 831 of file bgzf.c.

int bgzf_mt	(	BGZF *	fp,
		int	n_threads,
		int	n_sub_blks
	)

Enable multi-threading (only effective on writing and when the library was compiled with -DBGZF_MT)

Parameters

fp	BGZF file handler; must be opened for writing
n_threads	#threads used for writing
n_sub_blks	#blocks processed by each thread; a value 64-256 is recommended

Definition at line 593 of file bgzf.c.

BGZF* bgzf_open	(	const char *	path,
		const char *	mode
	)

Open the specified file for reading or writing.

Definition at line 155 of file bgzf.c.

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.

Parameters

fp	BGZF file handler
data	data array to read into
length	number of raw bytes to read

Returns: number of bytes actually read; 0 on end-of-file and -1 on error

Definition at line 540 of file bgzf.c.

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.

Parameters

fp	BGZF file handler
data	data array to write
length	number of raw bytes to write

Returns: number of bytes actually written; -1 on error

Definition at line 755 of file bgzf.c.

ssize_t bgzf_read	(	BGZF *	fp,
		void *	data,
		size_t	length
	)

Read up to length bytes from the file storing into data.

Parameters

fp	BGZF file handler
data	data array to read into
length	size of data to read

Returns: number of bytes actually read; 0 on end-of-file and -1 on error

Definition at line 511 of file bgzf.c.

int bgzf_read_block ( BGZF * fp)

Read the next BGZF block.

Definition at line 384 of file bgzf.c.

int64_t bgzf_seek	(	BGZF *	fp,
		int64_t	pos,
		int	whence
	)

Set the file to read from the location specified by pos.

Parameters

fp	BGZF file handler
pos	virtual file offset returned by bgzf_tell()
whence	must be SEEK_SET

Returns: 0 on success and -1 on error

Definition at line 810 of file bgzf.c.

void bgzf_set_cache_size	(	BGZF *	fp,
		int	size
	)

Set the cache size. Only effective when compiled with -DBGZF_CACHE.

Parameters

fp	BGZF file handler
size	size of cache in bytes; 0 to disable caching (default)

Definition at line 792 of file bgzf.c.

int bgzf_useek	(	BGZF *	fp,
		long	uoffset,
		int	where
	)

Position BGZF at the uncompressed offset

Parameters

fp	BGZF file handler; must be opened for reading
uoffset	file offset in the uncompressed data
where	SEEK_SET supported atm

Returns 0 on success and -1 on error.

Definition at line 1031 of file bgzf.c.

long bgzf_utell ( BGZF * fp)

Position in uncompressed BGZF

Parameters

fp	BGZF file handler; must be opened for reading

Returns the current offset on success and -1 on error.

Definition at line 1082 of file bgzf.c.

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).

Parameters

fp	BGZF file handler
data	data array to write
length	size of data to write

Returns: number of bytes written (i.e., length); negative on error

Definition at line 732 of file bgzf.c.

Classes

Macros

Typedefs

Functions

Macro Definition Documentation

Typedef Documentation

Function Documentation