Merge pull request #179 from hammerlab/slo

indels PoC, take 2
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
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