hiReadsProcessor (version 1.8.2)

startgfServer: Start/Stop a gfServer instance

Description

Start or Stop a gfServer with indexed reference genome to align batch of sequences using BLAT gfServer/gfClient protocol.

Usage

startgfServer(seqDir = NULL, host = "localhost", port = 5560,
  gfServerOpts = c(repMatch = 112312, stepSize = 5, tileSize = 10, maxDnaHits
  = 10))
stopgfServer(host = "localhost", port = NULL)

Arguments

seqDir

absolute or relative path to the genome index (nib/2bit files).

host

name of the machine to run gfServer on. Default: localhost

port

a port number to host the gfServer with. Default is 5560.

gfServerOpts

a character vector of options to be passed to gfServer command on top of server defaults. Default: c(repMatch=112312, stepSize=5, tileSize=10, maxDnaHits=10). Set this to NULL to start gfServer with defaults.

Value

• system command status for executing gfServer command.

See Also

stopgfServer, read.psl, blatSeqs, read.blast8

Examples

#startgfServer(seqDir="/usr/local/blatSuite34/hg18.2bit",port=5560)
#stopgfServer(port=5560)