Multiple sets of FASTQ files

[superbobry]

The current documentation states that it's possible to pass a bunch of paired reads, eg

$ bwameth.py --reference $REF foo_1.fastq,foo_2.fastq bar_1.fastq,bar_2.fastq
Traceback (most recent call last):
  File "/home/user/.virtualenvs/env/bin/bwameth.py", line 581, in <module>
    main(sys.argv[1:])
  File "/home/user/.virtualenvs/env/bin/bwameth.py", line 576, in main
    rname(*args.fastqs), calmd=args.calmd,
TypeError: rname() takes at most 2 arguments (3 given)

However, args.fastqs are handled in way which makes this use-case impossible.

[superbobry]

I think I misread the documentation, sorry.

To prevent this kind of errors, I think it would be nice if bwameth accepted paired reads in a way similar to Bowtie:

$ bwameth.py --reference $REF -1 foo_1.fastq, bar_1.fastq -2 foo_2.fastq, bar_2.fastq

[brentp]

@superbobry it handles them like this:

bwameth.py --reference $REF foo_1.fastq,bar_1.fastq foo_2.fastq,bar_2.fastq

Does that work for you?

[superbobry]

Yes, this worked, thank you. My proposal was to make bwameth more robust to this kind of errors by adding separate -1 and -2 arguments for paired mode.

[brentp]

closing this as I'd like to keep the simplicity of positional args for the most common case.