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
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 #163 from hammerlab/variant-genotype

New genotype and somaticgenotype to store more intermediate statistics