Merge pull request #222 from hammerlab/bump-java-to-1.8-in-pom

Bump java version dependency in pom 1.7 -> 1.8
adding yourkit image
Merge pull request #226 from hammerlab/yourkit

Adding yourkit image
get reference as seq bytes from mdtag
Merge pull request #220 from hammerlab/md-tag-bytes

get reference as seq bytes from mdtag
Merge pull request #227 from hammerlab/pileup-elements-should-be-vector-not-list

Speedup Pileup.atGreaterLocus by using a vector for PileupElement
Remove == and equals() methods from Allele class

Since this is a case class, methods are automatically provided that implement
the same logic.
Refactor likelihood calculation

This commit 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.

Closes #228.
Change Likelihood computation to use the Colt library.