Make just one q-score-joined work for all input types

Took me a lot of head scratching to realize that there was a pair of qscore-joined methods, one for single end and one for paired. While I appreciate there are very good reasons for separating out functions dealing with distinct input types, in this case it doesn’t look like either the SE or PE qscore filtering accepts any different arguments. I’d find it easier to just use one function and having the program interpret the file type directly and performing the same operation regardless, but perhaps that creates headaches elsewhere.

Thanks for the suggestion @devonorourke! You hit the nail on the head: we agree having one command would be easiest for all, but it does create big headaches in other ways (namely, we need to create a TypeMap so that action input types can determine output types). This is something we are working on and some day in the future (a 2019 release perhaps) the dream will be a reality.


Got it.
What’s particularly confusing at first glance in this case is that the input for q-score can be paired end sequence data, but q-score-joined is for data presumably derived from paired end data, just joined already!
Thanks for the help