Bugs with WGS read strandedness and R1/R2 FASTQ output #39
Description
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.