#' starLong
#' run the STARlong mapping
#'
#' @param genomeDir character value indicating the location of STAR genome indexes
#' @param LR character value indicating the long read file
#' @param outputDir character value indicating the directory of output
#' @param cores integer value indicating the number of cores for parallel computing
#' @param SJ character value for 2pass STAR mapping
#'
#' @return
#' @export
#'
#' @examples
starLong = function( genomeDir , LR , outputDir , cores=10 , SJ=NULL )
{
STAR2bSMRT.dir = system.file(package = "STAR2bSMRT")
if( is.null(SJ) )
{
func = paste0("source " , STAR2bSMRT.dir , "/data/starLong1.sh")
sh = paste( func , genomeDir , LR , outputDir , cores )
runSH(sh)
} else {
func = paste0("source " , STAR2bSMRT.dir , "/data/starLong2.sh")
sh = paste( func , genomeDir , LR , outputDir , cores , SJ )
runSH(sh)
}
}
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