text: #!/usr/bin/env python
  __author__ = 'Sergei F. Kliver'
  import os
  import argparse
  
  from RouToolPa.Routines import SequenceRoutines
  
  
  parser = argparse.ArgumentParser()
  
  parser.add_argument("-r", "--reference", action="store", dest="reference", required=True,
                      help="File with reference genome")
  parser.add_argument("-s", "--samtools_directory", action="store", dest="samtools_dir", default="",
                      help="Directory with samtools binaries")
  parser.add_argument("-p", "--picard_directory", action="store", dest="picard_dir", default="",
                      help="Directory with PICARD jar")
  
  args = parser.parse_args()
  
  
  SequenceRoutines.prepare_reference_for_GATK(args.reference,
                                              picard_dir=args.picard_dir,
                                              samtools_dir=args.samtools_dir)
  