Added new CalledGenotype and CalledSomaticGenotype (+ serializers) to save more intermediate; changed string to seq[byte] for alleles
adding filters for somatic
add and fix comments and help messages
pr feedback; comment updates; alignment; alternateBase -> alternateBases
separated calledgenotype calledsomaticgenotype; separated genotypeconversions
updating assertbases function to compare strings
drop spark args and setting spark properties through code
codify args4j dependency
Merge pull request #172 from hammerlab/args4j

codify args4j dependency
remove unused imports
avoid making multiple SparkContexts in tests

this seems to have been the cause of a crazy nondeterministic
failure of DistributedUtilSuite.
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
Fix BayesianQualityVariantCaller merge mistake
Merge pull request #173 from hammerlab/test-fix

avoid making multiple SparkContexts in tests
Merge pull request #163 from hammerlab/variant-genotype

New genotype and somaticgenotype to store more intermediate statistics
Removed check for correlated (nearby) SNVs from caller - moved this to a second pass over genotypes in some window