remove stale javadoc about removed cigar idx field
change a couple PileupElement Longs to Ints

they're actually Ints
dangle a couple of close-parends
Merge pull request #166 from hammerlab/ints

change a couple PileupElement Longs to Ints
better debuggability for some test assertions
remove semicolon from test case name

seems to trip up intellij
dangle close-parend
fix deprecation warnings
remove some unused test helper functions
Table-ify a PileupSuite case
Merge pull request #167 from hammerlab/test-nits

Remove more deprecation warnings; some test nits
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
Removed check for correlated (nearby) SNVs from caller - moved this to a second pass over genotypes in some window
update tests and parameters
adding average mapping quality and average base quality filters