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) if MUT_RATE < 0.: MUT_RATE = None # sequencing error model # if SE_RATE < 0.: SE_RATE = None if SE_MODEL == None: print 'Using default sequencing error model.' SE_MODEL = SIM_PATH+'/models/errorModel_toy.p' SE_CLASS = ReadContainer(READLEN,SE_MODEL,SE_RATE) else: # probably need to do some sanity checking
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) if MUT_RATE < 0.: MUT_RATE = None # sequencing error model # if SE_RATE < 0.: SE_RATE = None if SE_MODEL == None: print 'Using default sequencing error model.' SE_MODEL = SIM_PATH+'/models/errorModel_toy.p' SE_CLASS = ReadContainer(READLEN,SE_MODEL,SE_RATE) else: # probably need to do some sanity checking