updated infer.clonality and the evaluation driver scripts so as to be more efficient. Breaks backward compatibility in the usr options. Now, the user provided squared errors, and any memomized internal computations are passed inthrough a parameter called internal.parameters. Also added a looping option to the evluation driver script, so as to not overload the job assigner and qsub torque servers
updated documentation and stderr bugs
fixed stderr bug in infer.clonality