fai_open: Open a faidx-indexed FASTA file

In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description

Opens a FASTA file that has an associated .fai index file

Usage

fai_open( filename )

Arguments

filename

File name of the FASTA file. A file filename.fai is expected to reside in the same path.

Details

Use .Call("FAI_open", filename ) to eliminate the slight overhead of using the R wrapper function.

Value

Returns a FAIhandle that is required for fai_query3, fai_query5, fai_close

Author(s)

Ulrich Wittelsbuerger

See Also

fai_reopen, fai_query3, fai_query5

Examples

##
##	Example :
##
faifile  <- system.file("extdata", "ex.fasta", package = "WhopGenome")
faifh <- fai_open( faifile )
stopifnot( !is.null(faifh) )

WhopGenome documentation built on May 1, 2019, 10:12 p.m.