Bugs with WGS read strandedness and R1/R2 FASTQ output

[solveforj]

I would like to report two bugs.

WGS strandedness bug: The first has to do with the strandedness of WGS reads. At this line of code, it should be:

ss = ss.reverse_complement(id=True, description=True)

Currently, R1 is always on the + strand and R2 is always on the - strand. I have noticed that it seems intentional (not due to a bug) in the source code that for PL reads, R1 is always + and R2 is always -. Is there a reason for this?

R1/R2 FASTQ output bug: At this line, args.output_name is not defined, so if you specify --dist as a command line argument, the program will fail.