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.
Thanks, good call @arahuja . Updating now to use a DenseDoubleMatrix2D from colt: http://en.wikipedia.org/wiki/Colt_(libraries)