Removed check for correlated (nearby) SNVs from caller - moved this to a second pass over genotypes in some window
Merge pull request #170 from hammerlab/somlogodds-update

Move removing nearby or correlated snps to second pass
refactor PileupElement, elementAtGreaterLocus

- elementAtGreaterLocus was mimicking the vals in PileupElement;
  cleaner to advance through loci by making new PileupElements
  at each CigarElement
- keep all CigarElements around in PileupElement; track current
  idx into that array
  - used especially in indel code downstream
- correctly handle insertions at the start of a contig (include
  trailing reference base)
- correctly handle insertions at the start of a read (skip them;
  they don't count for reference locus that lands at the first
  read-base after them)
import nits
remove PileupElement.sequencedSingleBaseOpt

doesn't generalize well to an insertion-capable world, and isn't
really that useful anyway.
generalize ReferenceVariant to multiple ref bases

in preparation for broader Deletion support
add simple insertion-calling

IndelPoCCaller can now call both.

Next step: working deletion and insertion calling into existing
callers.
push PileupElement.sequencedBases into Alignment

expand Alignment hierarchy to expose `sequencedBases` and
`referenceBases`
push `possibleAlleles` computation into Pileup
push `Allele` concept into `PileupElement`
generalize Alleles to contain refBases & altBases
bump to ADAM 0.13.1-SNAPSHOT for MD tag fix
push `possibleAlleles` into `Pileup`