Bendycar
commented
1 month ago Hi Lena,
Thanks for your feedback! I think you're totally right about the order thing -- I outlined the main code before I realized the get_position function needs to work differently depending on strandedness, so I didn't take that into account initially! Thanks for pointing that out, it's a sneaky detail that I might have missed!
Hi Ben!
This is incredibly thorough pseudocode - great job! I like the way you chose to split up the extraction of chromosome, position, strandedness, and UMI into different functions. I did this all in one function, which could potentially get unreadable/messy, so I like your approach much better. I also like the way that you included your get_args() function - that is a very nice touch!
I'm struggling to find room for improvement in the pseudocode itself. It addresses all the major aspects of the problem! But, I wonder if you will need to get_strandedness() before you get_position(). Currently, you get_position() right on the line immediately prior to get_strandedness(). I think this will be necessary because I think your get_position() function will need to adjust for soft clipping differently depending strandedness. However, I could be completely misunderstanding this.
I hope this makes sense, and great job again!