custom = {(reads mapped to scaffold)/(total reads for sample)}/(length of scaffold)

def calc_custom(custom, genome, scaffold, sequence, scaffold_coverage, total_bases):
	"""
	custom = {(reads mapped to scaffold)/(total reads for sample)}/(length of scaffold)
	"""
	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