#' kallistoQuant
#' perform the kallisto transcript quantification
#' @param transcript character value indicating the transcriptome file
#' @param SR1 character value indicating the short read file in fastq format:
#' single-end or paired-end R1
#' @param SR2 character value indicating the short read file in fastq format:
#' paired-end R2
#' @param outputDir character value indicating the direcotry where results are
#' saved.
#'
#' @return
#' @export
#'
#' @examples
kallistoQuant = function( transcript , SR1 , SR2 , outputDir )
{
STAR2bSMRT.dir = system.file(package = "STAR2bSMRT")
func = paste0("source " , STAR2bSMRT.dir , "/data/kallistoQuant.sh")
sh = paste( func , transcript , SR1 , SR2 , outputDir )
runSH(sh)
read.table( paste0(outputDir,"/output/abundance.tsv") , header=T )
}
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