better error msg for TestUtil.assertAlmostEqual
use .sum instead of .reduce(_ + _)
correct and simplify ploidy calculation
possibleAlleles, possibleGenotypes into Pileup

also rename to `possibleGenotypes`, which is more apt
push `Allele` concept into `PileupElement`
upgrade to ADAM 0.14.0
push PileupElement.sequencedBases into Alignment

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

requires ADAM 0.14.0 MD-tag fix
generalize Alleles to contain refBases & altBases
move likelihood calcs into GenotypeAlleles, 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
rename Bayes' Suite to PileupLikelihoodSuite

it's actually just testing Pileup functionality now