tabix_setregion: Reopen a Tabix-indexed file if the filehandle became invalid.
In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	tabix_setregion( tabfh, tid, beginpos, endpos )

`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

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

Tabix file handle

Ulrich Wittelsbuerger

tabix_open

##
##	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