Output trimmed and excluded reads to separate output files

For QC purposes, it is often important to see what part of a read got trimmed off and which reads were excluded due to quality filters. There should be an option to write separate fasta/fastq files with these items.

I have forked skewer and implemented this for paired-end, non-barcoded input only. I could submit a patch, but I imagine you'll want to implement it in a more general way. For trimmed reads, I write fastq output that has the trimmed bases in lower-case. For excluded reads, I write a separate fastq that has the entire read, but the ID line also contains the TAG describing why it was excluded.

relipmoc / skewer

Output trimmed and excluded reads to separate output files #5