tabix_read: Read a line from a tabix_open()'ed file
In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

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

Read a line from a tabix_open()'ed file

1 2	tabix_read( tabfh ) tabix_readraw( tabfh )

tabfh

Tabix file handle as returned by tabix_open

Instead of tabix_readraw() you can use .Call("tabix_readLine", tabfh ) to eliminate the slight overhead of using the R wrapper function.

A line of data from the indexed data file. tabix_read splits the line up into its fields and returns a vector. tabix_readraw returns the line as stored in the file.

Ulrich Wittelsbuerger

tabix_open

##
##	Example : (NOT RUN)
##

print("Opening and reading")
gffgzfile  <- system.file("extdata", "ex.gff3.gz", package = "WhopGenome" )
if( file.exists(gffgzfile) )
{
 gffgzfile
 gffh <- tabix_open( gffgzfile )
 gffh
 stopifnot( !is.null(gffh) )
 tabix_read( gffh )
 tabix_close( gffh )
 gffh
}