code: def calc_custom(custom, genome, scaffold, sequence, scaffold_coverage, total_bases):
  	
  	index = 0
  	if scaffold in scaffold_coverage: # what if the scaffold does not have bases mapped back to it? (this *should* not happen)
  		if genome not in custom:
  			custom[genome] = [[] for i in scaffold_coverage[scaffold]]
  		for cov in scaffold_coverage[scaffold]:
  			length = float(len(sequence[1]))
  			bases = cov * length
  			custom_value = ((bases) / (total_bases[index])) / length
  			custom[genome][index].append(custom_value)
  			index += 1
  	return custom
docs: custom = {(reads mapped to scaffold)/(total reads for sample)}/(length of scaffold)