Fixing PairHMM and refactor of test routines

-- Fixed Logless bug as suggested by Diego and Scott
-- Fixed '-all' option to run all implementations without keeping it all in memory
-- Fixed the option to run with multiple test cases
-- Restructured input/ouput to work from different files
-- Evaluate doesn't test correctness anymore, it outputs the likelihoods for downstream testing, output now goes to a uniquely named file prefixed by the hmm class name (e.g. LoglessPairHMM.7.out)
-- Separated input dataset (.in) from output dataset (.out). Truth can always be re-generated by running with --standard
-- Renamed implementations with more indicative names of what they actually do
-- Added description of exact features differentiating each implementation
-- Refactored logger output

The test files are now immutable (since the output is separate) and are avaiable in the public dropbox (will send link via e-mail soon). The truth output can always be re-generated by the StandardPairHMM, but I will provide ground truth files in the public dropbox as well.
New scripts to test sensitivity and accuracy

-- added checkLikelihoods lua script to compare two outputs (likelihood sensitivity test -- default 0.001)
-- added checkHaplotypes lua script to check if the maximum likelihood haplotype in two implementations is the same (accuracy test)

The sensitivity test is ready to use, but I am still working on the haplotype check script. The idea here is to check that different implementations of the PairHMM always choose the same most likely haplotype for each batch of N reads and M haplotypes
checkHaplotypes implementation

Use this script to check if your implementation is choosing the same most likely haplotypes for each block of N reads and M haplotypes.

Usage:
  lua checkHaplotypes <test.in> <expected.out> <actual.out>
Fixed issue with output not writing all tests
working on scripts
Merge branch 'master' of github.com:MauricioCarneiro/PairHMM into feature/rootbeer

Conflicts:
	.gitignore
	src/main/java/org/broadinstitute/Evaluate.java