WhopGenome (version 0.9.4)

tabix_setregion: Reopen a Tabix-indexed file if the filehandle became invalid.

Description

Reopen a Tabix-indexed file if the filehandle became invalid.

Usage

tabix_setregion( tabfh, tid, beginpos, endpos )

Arguments

tabfh

Tabix handle, once returned by tabix_open

tid

A string naming one of the contig/chromosome identifiers stored in the Tabix indexed file

beginpos

Earliest position from which subsequent tabix_read/tabix_readraw calls return lines

endpos

Last position to return lines from with tabix_read/tabix_readraw

Value

Tabix file handle

Details

Use .Call("tabix_setRegion", tabfh, tid, beginpos, endpos ) to eliminate the slight overhead of using the R wrapper function.

See Also

tabix_open

Examples

##
##	Example :
##
gffgzfile  <- system.file("extdata", "ex.gff3.gz", package = "WhopGenome" )
gffh <- tabix_open( gffgzfile )
gffh
tabix_setregion( gffh, "ex.1", 1, 400 )
tabix_close( gffh )
gffh