Phil's Peer Review

[philmcnamara]

Good example of input and output file to clarify what's happening with the code.

Interesting idea to sort by the QNAME with the -n flag, but because the UMI is last it will sort by all the numbers first, everything in parentheses below:

(NS500451:154:HWKTMBGXX:1:11101:24260:1121:)CTGTTCAC

This could maybe still work if you mess around with regex/sed to get the umi in its own field? Resetting memory every time we finish with an UMI would definitely be efficient.

Nice standalone functions to extract the data, but not sure it's worth making a function to open the file since we'll only be doing it once.