fai_build

Build index for a FASTA or razip compressed FASTA file.

fai_destroy

Distroy a faidx_t struct.

fai_load

Load index from "fn.fai".

fai_fetch

Fetch the sequence in a region.

Build index for a FASTA or razip compressed FASTA file.

void fai_build(
    const char *fn);  

Parameters

fn

FASTA file name

Discussion

File "fn.fai" will be generated.

Distroy a faidx_t struct.

void fai_destroy(
    faidx_t *fai);  

Parameters

fai

Pointer to the struct to be destroyed

Load index from "fn.fai".

faidx_t *fai_load(
    const char *fn);  

Parameters

fn

File name of the FASTA file

Fetch the sequence in a region.

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

Parameters

fai

Pointer to the faidx_t struct

reg

Region in the format "chr2:20,000-30,000"

len

Length of the region

Return Value

Pointer to the sequence; null on failure

Discussion

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

© The Wellcome Trust Sanger Institute. Last Updated: Saturday, June 13, 2009