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"

Go to the source code of this file.

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_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)

Macro Definition Documentation

#define kroundup32

(

x)

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

Definition at line 31 of file faidx.c.

Function Documentation

FILE* download_and_open

(

const char *

fn)

Definition at line 206 of file faidx.c.

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.

faidx_t* fai_build_core

(

BGZF *

bgzf)

Definition at line 50 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.

faidx_t* fai_read

(

FILE *

fp)

Definition at line 137 of file faidx.c.

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

Definition at line 121 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.