refactor into cli package for any commands, basic API-style classes kept separate. Also added base classes for commands to track help, verbose, and outputs
renamed stub script to avoid confusion
Reorg filters a bit more, added seqtrim filter (adapters)
Added option for applying filter to read1 or read2. This way we could
use the same filter class, but apply two different filters to interlaced
files.
Initial StringUtils to add (preliminary) splicing and counts