I do not think izip will accomplish what we need to do here (I tried using it at first but could not figure out a way to do so). There will be more fastq records in the index-reads file then there will be in the joined-reads file. Simply because not all paired-ends will join. So, I need to iterate through the index-reads more than I will the joined-reads. Basically, both files will be in the same order except for those missing records in the joined-reads file.So, the nested while loop was intentional.