Paired read processing

[Colelyman]

The algorithm runs the unit tests successfully now, I imagine that it needs to be integrated into the core so that the newly aligned reads are actually used, right? If so, could you point me to where this would need to be done?

[Colelyman]

@kclem I have fixed the bugs in the get_consensus_alignment_from_pairs function (according to the test cases and running the nhej example), but now I get an error here https://github.com/edilytics/CRISPResso2/blob/upstream-paired-processing/CRISPResso2/CRISPRessoCORE.py#L2619

It is trying to take the reverse complement of variant which is ACTG...+ACTG... and it is obviously failing on the +. I assume the sequences on either side of the + are R1 and R2. Is the right thing to do separate the variant on the +?

But I have a suspicion that we will need to implement some more logic to check for the reverse complement of both reads...