old_contents: import Fast5File
  import sys
  
  def run(parser, args):
  	
  	for fast5 in Fast5File.Fast5FileSet(args.files):
  
  		if args.start_time or args.end_time:
  			read_start_time = fast5.get_start_time()
  			read_end_time = fast5.get_end_time()
  			if args.start_time and args.start_time > read_start_time:
  				fast5.close()
  				continue
  			if args.end_time and args.end_time < read_end_time:
  				fast5.close()
  				continue
  
  		fas = fast5.get_fastqs(args.type)
  		if args.high_quality:
  			if fast5.get_complement_events_count() <= \
  			   fast5.get_template_events_count():
  				fast5.close()
  				continue
  
  		for fa in fas:
  			if fa is None or \
  			len(fa.seq) < args.min_length or \
  			len(fa.seq) > args.max_length and \
  			args.max_length > 0:			
  				continue
  
  			print fa
  
  		fast5.close()
  
  
new_contents: import Fast5File
  import sys
  
  def run(parser, args):
  	
  	for fast5 in Fast5File.Fast5FileSet(args.files):
  
  		if args.start_time or args.end_time:
  			read_start_time = fast5.get_start_time()
  			read_end_time = fast5.get_end_time()
  			if args.start_time and args.start_time > read_start_time:
  				fast5.close()
  				continue
  			if args.end_time and args.end_time < read_end_time:
  				fast5.close()
  				continue
  
  		fas = fast5.get_fastqs(args.type)
  		if args.high_quality:
  			if fast5.get_complement_events_count() <= \
  			   fast5.get_template_events_count():
  				fast5.close()
  				continue
  
  		for fa in fas:
  			if fa is None or \
  			len(fa.seq) < args.min_length or \
  			(len(fa.seq) > args.max_length and \
  			args.max_length > 0):			
  				continue
  
  			print fa
  
  		fast5.close()
  
  
subject: Update fastq.py