def run(self):
		self.logToMaster("CreatePevntsFile\n") 
		opts=self.options
		if opts.simulation:
			truefile=os.path.join(opts.cnavgout, "true.braney")
			truehist=os.path.join(opts.cnavgout, "HISTORIES_0.braney") 
			subprocess.call("grep -v ^$ %s | gzip > %s" % (truefile, truehist), shell=True)
			make_STATS_from_truebraney(truefile, os.path.join(opts.cnavgout, "HISTORY_STATS_0"))
		historyScores=histseg.combine_history_statsfiles(opts.cnavgout)
		np.savetxt(self.historystatsfile, historyScores, fmt='%d', delimiter='\t')	
		totalp=histseg.compute_likelihood_histories(historyScores[:,0], historyScores)
		events=histseg.get_events_from_cnavgdir(opts.cnavgout, historyScores, totalp)
		pickle.dump(events, open(self.pevntsfile, 'wb'), pickle.HIGHEST_PROTOCOL)
def score_and_link_cycles(args):
	if args.binwidth: 
		histseg.Global_BINWIDTH=args.binwidth
	if not args.historystats and args.cnavg: 	
		historyScores=histseg.combine_history_statsfiles(args.cnavg)
	elif not os.path.isfile(args.historystats) and args.cnavg: 
		historyScores=histseg.combine_history_statsfiles(args.cnavg)
		np.savetxt(args.historystats, historyScores, fmt="%d", delimiter='\t')
	elif os.path.isfile(args.historystats):
		historyScores=np.loadtxt(args.historystats, dtype=int)
	if not historyScores: 
		sys.exit("Need to use --historystats or --cnavg option")
	totalp=0
	if args.totalp: 
		totalp=args.totalp
	else: 
		totalp = histseg.compute_likelihood_histories(historyScores[:,0], historyScores)
	allevents=[]
	if args.cnavg: 
		sys.stderr.write("using cnavg dir: %s\n" % (args.cnavg))
		allevents=histseg.get_events_from_cnavgdir(args.cnavg, historyScores, totalp)
	elif args.inpickle and os.path.isfile(args.inpickle): 
		sys.stderr.write("using pickle file\n")
		allevents=pickle.load(open(args.inpickle, 'rb'))
	sys.stderr.write("there are %d events\n" % (len(allevents)))
	if args.outpickle: 
		for event in allevents: 
			event.trim()
		eventfile= open(args.outpickle, 'wb')
		pickle.dump(allevents, eventfile, pickle.HIGHEST_PROTOCOL)
	if args.events: 
		eventfile=open(args.events, 'w')
		for evnt in allevents: 
			eventfile.write("%s" % (str(evnt)))
	# link the events...
	if args.links: 
		if not allevents: 
			sys.exit("Need events to link!  use --inpickle or --cnavg or --events")
		if not totalp: 
			sys.exit("Need a --totalp or --cnavg or --historystats options")	
		eventlinks = link_events_by_order_within_histories(allevents)
		linkfile=open(args.links, 'w')
		for link in eventlinks: 
			link.likelihood=histseg.compute_likelihood_histories(link.histories, historyScores)
			linkfile.write("%s" % (str(link)))