Likelihood refactor

Moves the likelihood calculation code from Pileup and Genotype into
a new singleton object.

This refactoring enables a more efficient implementation that resuses
computation between genotypes that share alleles. On my local tests, the
likelihood calculation is about 40% faster than the previous implementation.
Overall that gives about a 10% performance boost to variant calling.

 * Create a new package and singleton object Likelihood for likelihood calculation code.
 * Remove likelihood calculation code from Pileup and Genotype
 * Port tests from PileupLikelihoodSuite and GenotypeSuite into a new test suite LikelihoodSuite
 * Port variant callers to use new likelihood calculation function.
 * Remove == and equals() methods from Allele class.

Closes #228.
Any background on using Colt here? Advantages/disadvantages compared to other packages?  Curious to know more about it since if we introduce a dependency here it be good to use the same array/matrix library in the rest of the code.  Not a blocked on this PR just interested here about how it measures up.