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)

Typedef Documentation

typedef struct __faidx_t faidx_t

Definition at line 49 of file faidx.h.

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.

Definition at line 174 of file faidx.c.

void fai_destroy

(

faidx_t *

fai)

Distroy a faidx_t struct.

Parameters

fai	Pointer to the struct to be destroyed

Definition at line 164 of file faidx.c.

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.

Definition at line 300 of file faidx.c.

faidx_t* fai_load

(

const char *

fn)

Load index from "fn.fai".

Parameters

fn	File name of the FASTA file

Definition at line 246 of file faidx.c.

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

Definition at line 376 of file faidx.c.

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.

Definition at line 381 of file faidx.c.