wording
simplify usage message; include RTD link
change heading
replace ReadFilter with a ProcessedReadWriter

All the code that sends a read to a different output file depending on
different criteria (too long, too short, trimmed, not trimmed) is now in
this class. This makes it a lot easier to understand where there the reads
actually go.

Also, get rid of the 'twoheaders' handling in many places. Make twoheaders
an attribute of a Sequence instead, and let the Sequence deal with it.
Get rid of discard_untrimmed and discard_trimmed.

If reads should be discarded, the output files
(un)trimmed_(paired_)outfile are instead set to None.