Merge pull request #1 from veg/master

Added an option to output diagnostics to STDERR as JSON and synced the README file with the last option list
permit punching out of low-quality bases rather than splitting/truncating/etc
Merge branch 'master' of github.com:nlhepler/qfilt

Conflicts:
	src/argparse.cpp
	src/argparse.hpp
fix warning for signed/unsigned comparisons
Merge pull request #1 from nlhepler/master

Merging Lance's edits