leslie-c / deduper Goto Github PK

-Problem is well stated and concise. As the reader I can tell exactly what problem you are addressing. It might be helpful to include a quick statement of how your code will address the problem before you jump into it.

-General workflow gives a good overview of how your code will flow.

-For sort_SAM I'm pretty sure you can use a bash command that will sort your file

-Your get_UMI function is maybe a little too simplified to an outside reader. After reading through this and the main function I'm uncertain of it's prominent role and when you plan to call it. I would consider maybe explaining more, but I think in your actual code this will be a good function.

-get read info is well stated and defined. Good use of input and output.

-for the main_function, do you think keeping this a function or writing this as general code to help with memory storage will be better? I do think your structure and checks through the pseudocode are very logical and very easy to follow. It's easy to see how you are going to pass in your files, parse them, apply your duplicate checks, and then output to a "good or bad file". I feel like when you actually are writing your code you'll have a good structure to go off of. I think it would be helpful to add another little section after your functions to walk through how you plan to place and apply them.

I think you're on the right track though and your code is logically written and mostly easy to follow. If you have any questions or concerns with my statements feel free to reach out to me!