Qual updates

~~NOT READY FOR MERGE YET~~

Getting a lot of changes in for the improvement to ``parse_fastq`` where usable qual scores are returned. This is not ready for merge yet, most likely, it is just more effective to have Travis running the full test suite than it is to do locally. Most major failures (eg, `split_libraries_fastq`, `extract_barcodes`, `convert_fastafastq`, etc) are handled so far.