celalp

library(optparse)

option_list <- list( 
  make_option(c("-g", "--gtf"), action="store", help="gtf file to use"),
  make_option(c("-r", "--refflat"), action="store", help="refflat output"),
  make_option(c("-s", "--savedb"), action="store_true", help="save the intermediate txdb"),
  make_option(c("-d", "--dbname"), action="store", help="name for the txdb")
)

opt <- parse_args(OptionParser(option_list=option_list))