faidx.h File Reference

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Typedefs
typedef struct __faidx_t	faidx_t

Functions
int	fai_build (const char *fn)
void	fai_destroy (faidx_t *fai)
faidx_t *	fai_load (const char *fn)
char *	fai_fetch (const faidx_t *fai, const char *reg, int *len)
int	faidx_fetch_nseq (const faidx_t *fai)
char *	faidx_fetch_seq (const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)
int	faidx_has_seq (const faidx_t *fai, const char *seq)
int	faidx_nseq (const faidx_t *fai)
const char *	faidx_iseq (const faidx_t *fai, int i)
int	faidx_seq_len (const faidx_t *fai, const char *seq)

Typedef Documentation

typedef struct __faidx_t faidx_t

Function Documentation

int fai_build

(

const char *

fn

)

Build index for a FASTA or bgzip-compressed FASTA file.

Parameters

fn	FASTA file name

Returns

0 on success; or -1 on failure File "fn.fai" will be generated.

void fai_destroy

(

faidx_t *

fai

)

Distroy a faidx_t struct.

Parameters

fai	Pointer to the struct to be destroyed

char* fai_fetch	(	const faidx_t *	fai,
		const char *	reg,
		int *	len
	)

Fetch the sequence in a region.

Parameters

fai	Pointer to the faidx_t struct
reg	Region in the format "chr2:20,000-30,000"
len	Length of the region; -2 if seq not present, -1 general error

Returns

Pointer to the sequence; null on failure

The returned sequence is allocated by malloc family and should be destroyed by end users by calling free() on it.

faidx_t* fai_load

(

const char *

fn

)

Load index from "fn.fai".

Parameters

fn	File name of the FASTA file

int faidx_fetch_nseq

(

const faidx_t *

fai

)

Fetch the number of sequences.

Parameters

fai	Pointer to the faidx_t struct

Returns

The number of sequences

char* faidx_fetch_seq	(	const faidx_t *	fai,
		const char *	c_name,
		int	p_beg_i,
		int	p_end_i,
		int *	len
	)

Fetch the sequence in a region.

Parameters

fai	Pointer to the faidx_t struct
c_name	Region name
p_beg_i	Beginning position number (zero-based)
p_end_i	End position number (zero-based)
len	Length of the region; -2 if c_name not present, -1 general error

Returns

Pointer to the sequence; null on failure

The returned sequence is allocated by malloc family and should be destroyed by end users by calling free() on it.

int faidx_has_seq	(	const faidx_t *	fai,
		const char *	seq
	)

Query if sequence is present

Parameters

fai	Pointer to the faidx_t struct
seq	Sequence name

Returns

1 if present or 0 if absent

const char* faidx_iseq	(	const faidx_t *	fai,
		int	i
	)

Return name of i-th sequence

int faidx_nseq

(

const faidx_t *

fai

)

Return number of sequences in fai index

int faidx_seq_len	(	const faidx_t *	fai,
		const char *	seq
	)

Return sequence length, -1 if not present