Assignment-the-first comments

[amcrabtree]

• Personal preference here- demultiplexing seems complicated enough that it would serve best as a standalone program instead of a function call.
• Input and outputs are very clear, thank you.
• I think that, if either of the indexes in R2 or R3 are low quality score, both R1 and R4 records get sent to the low quality bins. Same for N’s and index hopping.
• Looks like there needs to be a condition for index hoping bins.
• If writing to files, a return statement for a function call is unnecessary (only needed if you’re returning a value).
• Indexes in R3 file are reverse complement of indexes in indexes.txt. Might be good to make a function for doing reverse complements.
• Consider using the indexes.txt file to have something to compare the indexes against in the sequencing file. Otherwise there may be mis-sequenced indexes which will create too many output bins.