Assignment 1 Comment

[norakearns]

Hi Nelson!
You may want to adjust your text files to have longer read lengths than your index files, just because it's a bit hard to differentiate them and it makes R1 and R4 appear like index files (although if this works for you that's totally fine!)
Also I think Leslie wants all your test files in the "TEST-input_FASTQ" and "TEST-output_FASTQ" folders.
One thing I noticed is that your pseudocode is lacking a section which identifies swapped reads and writes them to a swapped folder. At the top of your code you write that the output will include "2 FASTQ files: undermined/low quality of index 1 OR index 2" but then in your pseudocode you include low_quality_read_1/2 and undetermined_read_1/2 as separate files, and leave out the hopped_read1/2 files.
You may also want to specify a section in your pseudo code for how you will adjust the headers to include the indexes, and create some kind of architecture to store the indexes (like a set). Also you may want to include a function to reverse complement your index 2 before you check if they match!