Slight clarification to tool docstring & error msg as API changed
Use Biopython instead of Galaxy for FASTQ handling.

This was triggered by the hassle of running the script outside Galaxy.
Moreover, this ought to be faster with no object overhead.
Cleanup the wasteful plus lines in these FASTQ files.

Needed for the updated seq_select_by_id tool to pass, since it now
outputs the leaner FASTQ style.
Add WARNING/TODO note due to https://github.com/samtools/samtools/issues/313