upgrade to ADAM 0.14.0
better error msg for TestUtil.assertAlmostEqual
push PileupElement.sequencedBases into Alignment

expand Alignment hierarchy to expose `sequencedBases` and
`referenceBases`

requires ADAM 0.14.0 MD-tag fix
push `possibleAlleles` computation into Pileup
push `Allele` concept into `PileupElement`
generalize Alleles to contain refBases & altBases
push `possibleAlleles` into `Pileup`
move likelihood calculations into GenotypeAlleles
simplify and correct a ploidy bayes calculation
use .sum instead of .reduce(_ + _)
kill redundant likelihood-calc function

it had an incorrect calculation and was not used anyway
rename computeLikelihood
push Bayesian likelihood calcs into Pileup
lots of Bayes' Pileup/Genotype test cleanup

* remove genotypes that were not being checked
    * will follow on with GenotypeAlleles tests for these
    * assert that we are only checking the genotypes that are returned
* make the precision 1e-12
    * we were not always checking the right numbers previously, but were still within e.g. 1e-2.
    * fix the numbers we're checking
* a few general cleanups
    * common reference base / reads across test cases
    * use Table matchers