The problem with trouble shooting is that the trouble shoots back.

[The-Hungry-Caterpillar]

Hi Thai,
I like the level of detail you put into your code, but it is a little difficult to follow in such a form.
I couldn't tell, but did you have your loop set up in such a way that it checks UMI, then chromsome, then strand, then position (or some other order) instead of UMI and chromosome and strand and position?

Otherwise the code looks great!