Give a more useful error message if the threshold is set too low.


git-svn-id: https://svn.salilab.org/imp/trunk@17377 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Make 'reference' command available, and test it.


git-svn-id: https://svn.salilab.org/imp/trunk@17378 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Suppress "not used" warning.


git-svn-id: https://svn.salilab.org/imp/trunk@17379 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Add an example of using the 'reference' command.


git-svn-id: https://svn.salilab.org/imp/trunk@17380 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
suppress warnings

git-svn-id: https://svn.salilab.org/imp/trunk@17381 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
mark optparse as deprecated in docs

git-svn-id: https://svn.salilab.org/imp/trunk@17382 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
check for checks directly rather than use build level

git-svn-id: https://svn.salilab.org/imp/trunk@17383 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
no more fast build type

git-svn-id: https://svn.salilab.org/imp/trunk@17384 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
use new flag for running the example quickly

git-svn-id: https://svn.salilab.org/imp/trunk@17385 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
go off of checks level rather than build type

git-svn-id: https://svn.salilab.org/imp/trunk@17386 e91f8c7b-0e32-4433-a9ac-4502d39a4eab