Demultiplex Issues #3
Description
Hey Logan over all your pseudocode and logic looks pretty solid for this assignment. I'm only seeing a couple issues that I'll outline in bullet points below.
A) It seems that you are looping through you barcode file to create all of the files that you will need. Just make sure that you do this step twice for each Read R1 and R2.
B) In addition I don't believe the barcode file contains an entry for index-swapped reads or low quality score reads, so you will probably want to create these files outside of your file creation loop.
Other than those the only thing that I could think of that you might want to go further in to detail on is how you are going to grab each record from the fastq files and what function you will use to grab the first 4 lines of each and then pause while performing the rest of your logic on them.
Best,
Tyler