faidx.c File Reference

#include "config.h"
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include "htslib/bgzf.h"
#include "htslib/faidx.h"
#include "htslib/khash.h"
#include "htslib/knetfile.h"

Classes
struct	faidx1_t
struct	__faidx_t

Macros
#define	kroundup32(x)   (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))

Functions
faidx_t *	fai_build_core (BGZF *bgzf)
void	fai_save (const faidx_t *fai, FILE *fp)
faidx_t *	fai_read (FILE *fp)
void	fai_destroy (faidx_t *fai)
int	fai_build (const char *fn)
FILE *	download_and_open (const char *fn)
faidx_t *	fai_load (const char *fn)
char *	fai_fetch (const faidx_t *fai, const char *str, int *len)
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)
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)

Macro Definition Documentation

#define kroundup32

(

x

)

(--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))

Function Documentation

FILE* download_and_open

(

const char *

fn

)

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.

faidx_t* fai_build_core

(

BGZF *

bgzf

)

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

faidx_t* fai_read

(

FILE *

fp

)

void fai_save	(	const faidx_t *	fai,
		FILE *	fp
	)

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