text: """
  Author: Philippe Sanio
  Simple data generation with Survivor, minimap2, samtools and mosdepth
  """
  
  import sys, getopt, os
  import dataSimulation
  
  def main(argv):
     inputfile = ''
     outputfile = ''
     try:
         opts, args = getopt.getopt(argv,"hi:o:",["ifile=","ofile="])
     except getopt.GetoptError:
        print ('test.py -i <inputfile> -o <outputfile>')
        sys.exit(2)
     for opt, arg in opts:
        if opt == '-h':
           print ('test.py -i <inputfile> -o <outputfile>')
           sys.exit()
        elif opt in ("-i", "--ifile"):
           inputfile = arg
        elif opt in ("-o", "--ofile"):
           outputfile = arg
     print ('Input file is "', inputfile)
     print ('Output file is "', outputfile)
  
  def help():
      print("""
              Options:
              -r --refFile <path/to/refFile.fa>       locations of reference file
              -o --outDir <path/to/outdir>            output location for sim data
              -n --number <amount>                    amount of simulations
              """)
  def options(argv):
      reffile = ""
      outdir = os.getcwd()
      amount = 1
      try:
           opts, args = getopt.getopt(argv, "hr:n:o:",["help","refFile=","number=","outDir="])
      except getopt.GetoptError:
          help()
          sys.exit(2)
  
  
  
      for opt, arg in opts:
          if opt in ("-r", "--refFile"):
              reffile = arg
          elif opt in ("-o","--outDir"):
              outdir = arg
          elif opt in ("-n", "--number"):
              amount = arg
          else:
              help()
  
      result = dict()
      result["reffile"] = reffile
      result["outdir"] = outdir
      result["amount"] = int(amount)
      return result
  
  
  if __name__ == "__main__":
  
     result = options(sys.argv[1:])
     result["survivor"] ="../SURVIVOR-master/Debug/SURVIVOR"
     result["survivorparamfile"] ="../survivor/parameter_file"
     result["errorprofile"] = "../SURVIVOR-master/Debug/HG002_Pac_error_profile_bwa.txt"
     result["minimap2"] ="../minimap2-2.17_x64-linux/minimap2"
     result["samtools"] ="../samtools"
     result["mosdepth"] ="../mosdepth"
     print(result)
     ds = dataSimulation.dataSimulation(result)
  