add command line arguments to main

main will act as our runner and include information about training and
testing sets as well as number of threads

we need -std=c++11 to use stoi

hmm now has constructor which takes a filename
the tests include this new constructor

new timer file
	has ability to time a function, but currently can only time
	`perform_run`
	the function perform_run runs the forward algorithm on specified
	training and testing sets
changed c++11 to c++0x for travis
fixed comments from aaron

removed c++0x dependency by using atoi
using 2 spaces instead of 4
using getopt

main now uses getopt for arguments

Usage: ./bin/main -r train_file -t test_file [-n level_one_threads -m
level_two_threads]

closes #14
added test for omp nesting
added hmm::parallel_forward
added parallel run in `perform_run`
added script for generating test inputs
added a peformance test script
re-work so HMM isn't recreated each time