Support output to two files when operating in paired mode

[tfenne]

I know, I know, I'm the one who suggested making it mirror grep as much as possible. But I find that when grepping paired end fastqs it would be really nice to be able to write the matching read pairs to two separate files.

[nh13]

I this is a perfectly reasonable request with one caveat: if folks are providing multiple pairs of FASTQS (e.g. S1.R1.fq.gz, S1.R2.fq.gz, S2.R1.fq.gz, S2R2.fq.gz, ...) then I'd suggest you get only two separate files (R1 and R2), rather than the same number as the input files, unless it is easy to code. Thoughts?

[tfenne]

Agreed - just a single pair of output files. You can always just shell loop over input pairs if you want output files per set of input files.

[nh13]

#30