6d7cc6e2fecade5cd9a66ab29452131dcb1d618e,bin/basenji_sad_ref_multi.py,,main,#,46

Before Change

      default="%s/data/hg19.fa" % os.environ["BASENJIDIR"],
      help="Genome FASTA for sequences [Default: %default]")
  parser.add_option("-g", dest="genome_file",
      default="%s/data/human.hg19.genome" % os.environ["BASENJIDIR"],
      help="Chromosome lengths file [Default: %default]")
  parser.add_option("--local",dest="local",
      default=1024, type="int",

After Change

  parser.add_option("-f", dest="genome_fasta",
      default="%s/data/hg19.fa" % os.environ["BASENJIDIR"],
      help="Genome FASTA for sequences [Default: %default]")
  parser.add_option("--flip", dest="flip_ref",
      default=False, action="store_true",
      help="Flip reference/alternate alleles when simple [Default: %default]")
  parser.add_option("--local",dest="local",
      default=1024, type="int",
      help="Local SAD score [Default: %default]")
  parser.add_option("-n", dest="norm_file",

Instances