[DOC] Fixing dox such that it can be built without crashing dox.
[DOC] Starting to add documentation for stream module.

The parts that I could not write documentation for are annotated with
TODOs.  Also includes partial documentation in basic that I needed to
point to.

Plus one fix for dox.
[FEATURE,API] Refactorization of ucsc_io module.

Adding SmartFile for Ucsc format, besides others.

I/O in store module is a bit clunky.

Most of the tests were duplicates, I do not know what the original
author intended.
[DOC] Adding dox for modules ucsc_io and gff_io.
Merge pull request #58 from holtgrewe/feature/stream/new-dox

Some dox for the new stream module