Merge pull request #162 from hammerlab/seqbyte-bases

updating arrybyte to seqbyte
use .headOption
rm unused PileupElement.cigarElementIndex field
Merge pull request #165 from hammerlab/cigar-idx

Remove unused PileupElement field
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