Various improvements and add-ons, especially on amplian.py.

Changes:
- slightly better logging everywhere (no log on empty calls)
- better options help
- snv.py is now called from within dec.py and so always runs
- shorah.py now selects the highest frequency haplotypes and writes
them to a different file
- dec.py now keeps files by default and has an improved workflow,
resulting in less problems when rerunning. Snv directories are not
deleted when rerun
- amplian.py now runs snv.py, discovers highest entropy region and,
with matplotlib, also plots it