RNG_SEED = args.rng if RNG_SEED == -1: RNG_SEED = random.randint(1,99999999) random.seed(RNG_SEED) """************************************************ **** INPUT ERROR CHECKING ************************************************""" checkFileOpen(REFERENCE,'ERROR: could not open reference',required=True) checkFileOpen(INPUT_VCF,'ERROR: could not open input VCF',required=False) checkFileOpen(INPUT_BED,'ERROR: could not open input BED',required=False) requiredField(OUT_PREFIX,'ERROR: no output prefix provided') if (FRAGMENT_SIZE == None and FRAGMENT_STD != None) or (FRAGMENT_SIZE != None and FRAGMENT_STD == None): print '\nError: --pe argument takes 2 space-separated arguments.\n' exit(1) """************************************************ **** LOAD INPUT MODELS ************************************************""" # mutation models # MUT_MODEL = parseInputMutationModel(MUT_MODEL,1) if CANCER: CANCER_MODEL = parseInputMutationModel(CANCER_MODEL,2)
RNG_SEED = args.rng if RNG_SEED == -1: RNG_SEED = random.randint(1,99999999) random.seed(RNG_SEED) """************************************************ **** INPUT ERROR CHECKING ************************************************""" checkFileOpen(REFERENCE,'ERROR: could not open reference',required=True) checkFileOpen(INPUT_VCF,'ERROR: could not open input VCF',required=False) checkFileOpen(INPUT_BED,'ERROR: could not open input BED',required=False) requiredField(OUT_PREFIX,'ERROR: no output prefix provided') if (FRAGMENT_SIZE == None and FRAGMENT_STD != None) or (FRAGMENT_SIZE != None and FRAGMENT_STD == None): print '\nError: --pe argument takes 2 space-separated arguments.\n' exit(1) """************************************************ **** LOAD INPUT MODELS ************************************************""" # mutation models # MUT_MODEL = parseInputMutationModel(MUT_MODEL,1) if CANCER: CANCER_MODEL = parseInputMutationModel(CANCER_MODEL,2)