drop spark args and setting spark properties through code
codify args4j dependency
Merge pull request #172 from hammerlab/args4j

codify args4j dependency
GenotypeAlleles takes referenceAllele at creation

- makes more sense than passing it in to all subsequent method calls
- will allow for generalizing to multiple alleles / multiple
  reference-base-sequences e.g. when supporting deletions
remove PileupElement.sequencedSingleBaseOpt

doesn't generalize well to an insertion-capable world, and isn't
really that useful anyway.
Merge pull request #171 from hammerlab/spark-submit

Drop spark args and setting spark properties through code
Merge pull request #174 from hammerlab/ga-refbase

GenotypeAlleles takes referenceAllele at creation
Merge branch 'master' of https://github.com/hammerlab/guacamole into variant-genotype

Conflicts:
	src/main/scala/org/bdgenomics/guacamole/callers/BayesianQualityVariantCaller.scala
	src/main/scala/org/bdgenomics/guacamole/callers/SomaticLogOddsVariantCaller.scala
	src/main/scala/org/bdgenomics/guacamole/variants/GenotypeAlleles.scala