push PileupElement.sequencedBases into Alignment

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

bump to ADAM 0.13.1-SNAPSHOT for 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
remove unused GenotypeAlleles method

assumed ploidy == 2 and wasn't used
push Bayesian likelihood calcs into Pileup
upgrade to ADAM 0.14.0
move from deprecated SAMFileReader to SamReader
fix Bayes tests
better error msg for TestUtil.assertAlmostEqual