Psuedocode feedback

[bayknight]

Good start, Ross. I think you have a decent framework but may be missing some key points.

If you use and UMI as a key youll only be able to store N=UMI count number of files. are you going to clear this out between chromosomes?

@ lines need to be stored in the output file.

Reverse reads need to be adjusted based on the CIGAR string as well.
Softclipping is not hte only thing needed to account for in CIGAR string for reverse reads.

"proper strand" is not determined by if its a forward or reverse read I believe.

I may have missed it but i didnt see any psuedo functions.

overall i still think this is a good framework and once you start implementing this the issues will get flushed out. I think some stuff regarding start position is confusing and will be clarified in class I think. The psuedocode was easy to read and i appreciate the example walkthrough you put in textblocks at the top. I think the Problem could have been expanded a bit, but was still pretty good. Good job, Ross!